# Use full power of Python in Slicer

**URL:** <https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162>\
**Category:** Support\
**Tags:** feature\
**Created:** [June 13, 2019, 4:23pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162 "2019-06-13T16:23:11Z")\
**Posts on this page:** 17\
**Page:** 1

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 13, 2019, 4:23pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/1 "2019-06-13T16:23:11Z")

</div>

Until recently, Slicer used a custom Python build that was not binary compatible with third-party Python packages. Now, in latest Slicer Preview release, any Python packages can be installed and used in Slicer (except those that in direct conflict with version of libraries that are bundled with Slicer).

Example: do curve fitting using scipy

1. Install scipy by typing in Slicer’s Python console:

`pip_install('scipy')`

1. Try a simple curve fitting example:

```auto
import numpy as np
from scipy.optimize import curve_fit

def func(x, a, b, c):
    return a * np.exp(-b * x) + c

# Define the data to be fit with some noise:
xdata = np.linspace(0, 4, 50)
y = func(xdata, 2.5, 1.3, 0.5)
np.random.seed(1729)
y_noise = 0.2 * np.random.normal(size=xdata.size)
ydata = y + y_noise

# Fit for the parameters a, b, c of the function func:
popt, pcov = curve_fit(func, xdata, ydata)

# Plot results
plotNodes = {}
plot([xdata, ydata, func(xdata, *popt)], xColumnIndex = 0, nodes = plotNodes)
plotNodes['chart'].SetTitle('Curve fit demo')
plotNodes['series'][0].SetName('noisy')
plotNodes['series'][1].SetName('fit: a=%5.3f, b=%5.3f, c=%5.3f' % tuple(popt))

```

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/c/8c91195b3027899cfb491615286b5e90e864d816.png)

This feature will be heavily utilized in the upcoming [Slicer tutorial “Deep learning and computer vision for real-time procedure annotation”](http://www.slicerigt.org/wp/cars-2019-tutorial/) at CARS conference next week, where tensorflow, keras, scikit-learn pacakges are used in Slicer for classification of images streamed in real-time.

Any questions, comments, suggestions are welcome.

---

<div class="post-metadata">

**Author:** ![Alex\_Vergara](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alex_vergara/32/15205_2.png) [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Post date:** [June 14, 2019, 10:08am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/2 "2019-06-14T10:08:47Z")

</div>

It would be really nice if you allow plotly, matplotlib, (whatever), graphs to be displayed and saved inside a plot Node (Feature request?)

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 14, 2019, 6:07pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/3 "2019-06-14T18:07:24Z")

</div>

> [@Alex\_Vergara](#):
>
> It would be really nice if you allow plotly, matplotlib, (whatever), graphs to be displayed and saved inside a plot Node

There are hundreds of plotting libraries in Python, they offer amazing amount of functionality but at the same time this entire area in Python is a huge mess. I would not venture into choosing a handful of them and trying to make them integrate into Slicer’s GUI. There can be some implementation difficulties, too, as these packages often include interactive GUI components that may conflict with Slicer’s GUI components. For example, matplotlib’s Qt GUI is probably incompatible with Slicer’s Qt version (it should still be possible to use matplotlib’s "agg’ backend and display the plot as a rendered image).

For now, I would keep relying on Slicer’s very sophisticated 2D and 3D visualization capabilities and somewhat less sophisticated interactive 2D plotting (which is very fast and directly can visualize plots from Slicer’s VTK-based data storage objects). We could improve plotting API in Slicer to make it a bit more user friendly (`slicer.util.plot()` is an attempt towards that - see the example above).

If somebody wanted to experiment with third-party plotting then that would be great. It would be interesting to learn about the experiences. If results are very promising then maybe some helper/adapter functions could be added to Slicer that would help using some plotting packages.

---

<div class="post-metadata">

**Author:** ![ungi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ungi/32/78573_2.png) [@ungi](https://discourse.slicer.org/u/ungi)\
**Post date:** [June 15, 2019, 2:07am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/4 "2019-06-15T02:07:59Z")

</div>

Matplotlib doesn’t work in Slicer, not even with ‘agg’ backend. I’ve just tried it today. But I agree with Andras, it would be impossible to choose which Python GUI tools to support in Slicer. A convenient workaround is to save data (e.g. numpy.save) and load it (e.g. numpy.load) in a standard Jupyter notebook that has visualization scripts with Matplotlib, etc.

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 15, 2019, 4:48am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/5 "2019-06-15T04:48:25Z")

</div>

I’ve just tried interactive plotting using matplotlib and it works fine for me on Windows. I just had to switch to WXAgg backend.

Setup:

```python
pip_install("matplotlib wxPython")

```

Example interactive plot using matplotlib:

```python
# Get a volume from SampleData and compute its histogram
import SampleData
import numpy as np
volumeNode = SampleData.SampleDataLogic().downloadMRHead()
histogram = np.histogram(arrayFromVolume(volumeNode), bins=50)

# Set matplotlib to use WXAgg backend
import matplotlib
matplotlib.use('WXAgg')

# Show a plot using matplotlib
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.plot(histogram[1][1:], histogram[0].astype(float))
ax.grid(True)
ax.set_ylim((0, 4e5))
plt.show(block=False)

```

For reference, to create a similar plot using Slicer’s plotting infrastructure:

```python
chartNode = plot(histogram, xColumnIndex = 1)
chartNode.SetYAxisRangeAuto(False)
chartNode.SetYAxisRange(0, 4e5)

```

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/7/d7e295728729990f9c3c1e841f573c16b01d2e26.png)

---

<div class="post-metadata">

**Author:** ![ungi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ungi/32/78573_2.png) [@ungi](https://discourse.slicer.org/u/ungi)\
**Post date:** [June 15, 2019, 5:04am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/6 "2019-06-15T05:04:42Z")

</div>

Thanks! This is good to know. Especially in Slicer Jupyter notebooks. When batch processing lots of data in Slicer in Jupyter notebooks, it will be good that the notebooks can archive matplotlib graphs to report on results!  
For single graphs like in your example, I agree that Slicer plots are much more practical to use.

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [June 15, 2019, 5:00pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/7 "2019-06-15T17:00:34Z")

</div>

FWIW, unfortunately on mac with today’s nightly the pip install works and reports no errors, but when running the example script it crashes with the trace pasted below.

```auto
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libpython3.6m.dylib 0x000000010624b134 PyUnicode_InternInPlace + 116
1 libpython3.6m.dylib 0x000000010626c3cc PyUnicode_InternFromString + 60
2 libpython3.6m.dylib 0x000000010621eaa0 PyObject_GetAttrString + 48
3 libpython3.6m.dylib 0x00000001061dd088 PyObject_CallMethod + 120
4 libCTKScriptingPythonWidgets.0.1.dylib	0x00000001016f0ed0 ctkPythonConsolePrivate::push(QString const&) + 144
5 libCTKScriptingPythonWidgets.0.1.dylib	0x00000001016f1f22 ctkPythonConsole::executeCommand(QString const&) + 18
6 libCTKWidgets.0.1.dylib 0x0000000101722243 ctkConsolePrivate::internalExecuteCommand() + 563
7 libCTKWidgets.0.1.dylib 0x0000000101721aa8 ctkConsolePrivate::keyPressEvent(QKeyEvent*) + 2120
8 org.qt-project.QtWidgets 0x0000000106d7ec90 QWidget::event(QEvent*) + 5104
9 org.qt-project.QtWidgets 0x0000000106e31c8d QFrame::event(QEvent*) + 45
10 org.qt-project.QtWidgets 0x0000000106e3b78c QAbstractScrollArea::event(QEvent*) + 364
11 org.qt-project.QtWidgets 0x0000000106f22127 QTextEdit::event(QEvent*) + 407
12 org.qt-project.QtWidgets 0x0000000106d458cd QApplicationPrivate::notify_helper(QObject*, QEvent*) + 301
13 org.qt-project.QtWidgets 0x0000000106d46ddd QApplication::notify(QObject*, QEvent*) + 797
14 libqSlicerBaseQTGUI.dylib 0x00000001010bf3d6 qSlicerApplication::notify(QObject*, QEvent*) + 22
15 org.qt-project.QtCore 0x000000010d9d9c84 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 164
16 org.qt-project.QtWidgets 0x0000000106d9daf7 0x106d35000 + 428791
17 org.qt-project.QtWidgets 0x0000000106d458cd QApplicationPrivate::notify_helper(QObject*, QEvent*) + 301
18 org.qt-project.QtWidgets 0x0000000106d46c47 QApplication::notify(QObject*, QEvent*) + 391
19 libqSlicerBaseQTGUI.dylib 0x00000001010bf3d6 qSlicerApplication::notify(QObject*, QEvent*) + 22
20 org.qt-project.QtCore 0x000000010d9d9c84 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 164
21 org.qt-project.QtGui 0x000000010d2fa2ee QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 174
22 org.qt-project.QtGui 0x000000010d2e095b QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 155
23 org.qt-project.QtGui 0x000000010d2dc3bc QWindowSystemInterface::flushWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 572
24 libqcocoa.dylib 0x0000000116f63aa3 0x116f41000 + 141987
25 libqcocoa.dylib 0x0000000116f63be8 0x116f41000 + 142312
26 com.apple.AppKit 0x00007fff4b533b9f -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 6840
27 com.apple.AppKit 0x00007fff4b531e9f -[NSWindow(NSEventRouting) sendEvent:] + 478
28 libqcocoa.dylib 0x0000000116f68217 0x116f41000 + 160279
29 com.apple.AppKit 0x00007fff4b3d2101 -[NSApplication(NSEvent) sendEvent:] + 2953
30 libqcocoa.dylib 0x0000000116f6e669 0x116f41000 + 185961
31 com.apple.AppKit 0x00007fff4b3bfee8 -[NSApplication run] + 755
32 libwx_osx_cocoau_core-3.0.0.4.0.dylib	0x000000012bf72edf wxApp::CallOnInit() + 143
33 _core.cpython-36m-darwin.so 0x000000012b417724 wxPyApp::_BootstrapApp() + 532
34 _core.cpython-36m-darwin.so 0x000000012b41b604 meth_wxPyApp__BootstrapApp(_object*, _object*) + 100
35 libpython3.6m.dylib 0x000000010621c00c _PyCFunction_FastCallDict + 172
36 libpython3.6m.dylib 0x000000010629ac0f call_function + 479
37 libpython3.6m.dylib 0x0000000106297632 _PyEval_EvalFrameDefault + 25826
38 libpython3.6m.dylib 0x000000010629bb19 _PyEval_EvalCodeWithName + 3641
39 libpython3.6m.dylib 0x000000010629c652 _PyFunction_FastCallDict + 802
40 libpython3.6m.dylib 0x00000001061dc8a8 _PyObject_FastCallDict + 360
41 libpython3.6m.dylib 0x00000001061dc9c5 _PyObject_Call_Prepend + 149
42 libpython3.6m.dylib 0x00000001061dc5f6 PyObject_Call + 102
43 libpython3.6m.dylib 0x0000000106233d7e slot_tp_init + 158
44 libpython3.6m.dylib 0x000000010622feb9 type_call + 313
45 libpython3.6m.dylib 0x00000001061dc875 _PyObject_FastCallDict + 309
46 libpython3.6m.dylib 0x000000010629ab09 call_function + 217
47 libpython3.6m.dylib 0x0000000106297632 _PyEval_EvalFrameDefault + 25826
48 libpython3.6m.dylib 0x000000010629bb19 _PyEval_EvalCodeWithName + 3641
49 libpython3.6m.dylib 0x000000010629c652 _PyFunction_FastCallDict + 802
50 libpython3.6m.dylib 0x00000001061dc8a8 _PyObject_FastCallDict + 360
51 libpython3.6m.dylib 0x00000001061dc9c5 _PyObject_Call_Prepend + 149
52 libpython3.6m.dylib 0x00000001061dc5f6 PyObject_Call + 102
53 libpython3.6m.dylib 0x0000000106297933 _PyEval_EvalFrameDefault + 26595
54 libpython3.6m.dylib 0x000000010629bb19 _PyEval_EvalCodeWithName + 3641
55 libpython3.6m.dylib 0x00000001062910fb PyEval_EvalCodeEx + 107
56 libpython3.6m.dylib 0x000000010620233d function_call + 381
57 libpython3.6m.dylib 0x00000001061dc5f6 PyObject_Call + 102
58 libpython3.6m.dylib 0x0000000106297933 _PyEval_EvalFrameDefault + 26595
59 libpython3.6m.dylib 0x000000010629bb19 _PyEval_EvalCodeWithName + 3641
60 libpython3.6m.dylib 0x000000010629c316 fast_function + 742
61 libpython3.6m.dylib 0x000000010629abe9 call_function + 441
62 libpython3.6m.dylib 0x0000000106297632 _PyEval_EvalFrameDefault + 25826
63 libpython3.6m.dylib 0x000000010629bb19 _PyEval_EvalCodeWithName + 3641
64 libpython3.6m.dylib 0x0000000106291084 PyEval_EvalCode + 100
65 libpython3.6m.dylib 0x000000010628e7e0 builtin_exec + 528
66 libpython3.6m.dylib 0x000000010621c00c _PyCFunction_FastCallDict + 172
67 libpython3.6m.dylib 0x000000010629ac0f call_function + 479
68 libpython3.6m.dylib 0x0000000106297632 _PyEval_EvalFrameDefault + 25826
69 libpython3.6m.dylib 0x000000010629c26e fast_function + 574
70 libpython3.6m.dylib 0x000000010629abe9 call_function + 441
71 libpython3.6m.dylib 0x0000000106297632 _PyEval_EvalFrameDefault + 25826
72 libpython3.6m.dylib 0x000000010629bb19 _PyEval_EvalCodeWithName + 3641
73 libpython3.6m.dylib 0x000000010629c316 fast_function + 742
74 libpython3.6m.dylib 0x000000010629abe9 call_function + 441
75 libpython3.6m.dylib 0x0000000106297632 _PyEval_EvalFrameDefault + 25826
76 libpython3.6m.dylib 0x000000010629c6ec _PyFunction_FastCallDict + 956
77 libpython3.6m.dylib 0x00000001061dc8a8 _PyObject_FastCallDict + 360
78 libpython3.6m.dylib 0x00000001061dc9c5 _PyObject_Call_Prepend + 149
79 libpython3.6m.dylib 0x00000001061dc875 _PyObject_FastCallDict + 309
80 libpython3.6m.dylib 0x00000001061dd1d4 callmethod + 180
81 libpython3.6m.dylib 0x00000001061dd0c4 PyObject_CallMethod + 180
82 libCTKScriptingPythonWidgets.0.1.dylib	0x00000001016f0ed0 ctkPythonConsolePrivate::push(QString const&) + 144
83 libCTKScriptingPythonWidgets.0.1.dylib	0x00000001016f1f22 ctkPythonConsole::executeCommand(QString const&) + 18
84 libCTKWidgets.0.1.dylib 0x0000000101722243 ctkConsolePrivate::internalExecuteCommand() + 563
85 libCTKWidgets.0.1.dylib 0x0000000101724afb ctkConsolePrivate::pasteText(QString const&) + 459
86 libCTKWidgets.0.1.dylib 0x0000000101724893 ctkConsolePrivate::insertFromMimeData(QMimeData const*) + 115
87 libCTKWidgets.0.1.dylib 0x00000001017213b9 ctkConsolePrivate::keyPressEvent(QKeyEvent*) + 345
88 org.qt-project.QtWidgets 0x0000000106d7ec90 QWidget::event(QEvent*) + 5104
89 org.qt-project.QtWidgets 0x0000000106e31c8d QFrame::event(QEvent*) + 45
90 org.qt-project.QtWidgets 0x0000000106e3b78c QAbstractScrollArea::event(QEvent*) + 364
91 org.qt-project.QtWidgets 0x0000000106f22127 QTextEdit::event(QEvent*) + 407
92 org.qt-project.QtWidgets 0x0000000106d458cd QApplicationPrivate::notify_helper(QObject*, QEvent*) + 301
93 org.qt-project.QtWidgets 0x0000000106d46ddd QApplication::notify(QObject*, QEvent*) + 797
94 libqSlicerBaseQTGUI.dylib 0x00000001010bf3d6 qSlicerApplication::notify(QObject*, QEvent*) + 22
95 org.qt-project.QtCore 0x000000010d9d9c84 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 164
96 org.qt-project.QtWidgets 0x0000000106d9daf7 0x106d35000 + 428791
97 org.qt-project.QtWidgets 0x0000000106d458cd QApplicationPrivate::notify_helper(QObject*, QEvent*) + 301
98 org.qt-project.QtWidgets 0x0000000106d46c47 QApplication::notify(QObject*, QEvent*) + 391
99 libqSlicerBaseQTGUI.dylib 0x00000001010bf3d6 qSlicerApplication::notify(QObject*, QEvent*) + 22
100 org.qt-project.QtCore 0x000000010d9d9c84 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 164
101 org.qt-project.QtGui 0x000000010d2fa2ee QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 174
102 org.qt-project.QtGui 0x000000010d2e095b QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 155
103 org.qt-project.QtGui 0x000000010d2dc3bc QWindowSystemInterface::flushWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 572
104 libqcocoa.dylib 0x0000000116f63aa3 0x116f41000 + 141987
105 libqcocoa.dylib 0x0000000116f63be8 0x116f41000 + 142312
106 com.apple.AppKit 0x00007fff4b533b9f -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 6840
107 com.apple.AppKit 0x00007fff4b531e9f -[NSWindow(NSEventRouting) sendEvent:] + 478
108 libqcocoa.dylib 0x0000000116f68217 0x116f41000 + 160279
109 libqcocoa.dylib 0x0000000116f6f1d0 0x116f41000 + 188880
110 com.apple.AppKit 0x00007fff4b713f99 -[NSMenu _performKeyEquivalentWithDelegate:] + 142
111 com.apple.AppKit 0x00007fff4b714169 -[NSMenu _performKeyEquivalentWithDelegate:] + 606
112 com.apple.AppKit 0x00007fff4b713b2b -[NSMenu performKeyEquivalent:] + 68
113 com.apple.AppKit 0x00007fff4bb99517 routeKeyEquivalent + 860
114 com.apple.AppKit 0x00007fff4b3d19a0 -[NSApplication(NSEvent) sendEvent:] + 1064
115 libqcocoa.dylib 0x0000000116f6e669 0x116f41000 + 185961
116 com.apple.AppKit 0x00007fff4b3bfee8 -[NSApplication run] + 755
117 libqcocoa.dylib 0x0000000116f6ae0d 0x116f41000 + 171533
118 org.qt-project.QtCore 0x000000010d9d5641 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 417
119 org.qt-project.QtCore 0x000000010d9da358 QCoreApplication::exec() + 392
120 0x0000000100d42cec main + 540
121 libdyld.dylib 0x00007fff7a2613d5 start + 1

```

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 15, 2019, 5:49pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/8 "2019-06-15T17:49:41Z")

</div>

Which call caused the crash? You may try `plot.show()` (without `block=False`). There are 15-20 backends, I would expect that at least a few of them works on Mac, too.

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [June 16, 2019, 7:31pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/9 "2019-06-16T19:31:02Z")

</div>

The wx version dies on this line:

```auto
fig, ax = plt.subplots()

```

But using Agg directly works on the mac as shown in the example below.

(For context, this example is only slightly updated from something I put on the [Slicer3 wiki page almost 10 years ago](https://www.slicer.org/wiki/Slicer3:Python#Matplotlib_plotting_functionality) when we first started playing with python packages in Slicer).

```auto
import matplotlib
matplotlib.use ( 'Agg' )
from pylab import *

t1 = arange(0.0, 5.0, 0.1)
t2 = arange(0.0, 5.0, 0.02)
t3 = arange(0.0, 2.0, 0.01) 

subplot(211)
plot(t1, cos(2*pi*t1)*exp(-t1), 'bo', t2, cos(2*pi*t2)*exp(-t2), 'k')
grid(True)
title('A tale of 2 subplots')
ylabel('Damped')

subplot(212)
plot(t3, cos(2*pi*t3), 'r--')
grid(True)
xlabel('time (s)')
ylabel('Undamped')
savefig ( 'MatplotlibExample.png' )

import Slicer
r = vtk.vtkPNGReader()
v = vtk.vtkImageViewer()
r.SetFileName( 'MatplotlibExample.png' )

v.SetColorWindow(255)
v.SetColorLevel(128)
v.SetInputConnection(r.GetOutputPort())
v.Render()

```

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/2/926a7f715da74a3eb67c3ab3263afb25a579e8b7.png)

---

<div class="post-metadata">

**Author:** ![Jan\_Alexander](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jan_alexander/32/6831_2.png) [@Jan\_Alexander](https://discourse.slicer.org/u/Jan_Alexander)\
**Post date:** [February 24, 2021, 10:47am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/10 "2021-02-24T10:47:04Z")

</div>

When I try to install _wxpython_ by using

```auto
pip_install('wxpython')

```

I get following error:

```auto
configure: error: in `/tmp/pip-install-6tksvgas/wxpython_713cfb256f5442bfa5b03be8be257a56/build/wxbld/gtk3':
    configure: error: no acceptable C compiler found in $PATH
    See `config.log' for more details
    Error running configure
    ERROR: failed building wxWidgets

```

What I have tried:

Adapt dockerfile to try to include needed packages while building the docker:

```auto
RUN /home/sliceruser/Slicer/bin/PythonSlicer -m pip install matplotlib SimpleITK
RUN /home/sliceruser/Slicer/bin/PythonSlicer -m pip install -U \
-f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/debian-8 \
wxPython

```

I am stuck. For me, It would be very useful to be able to use matplotlib next to the Slicer visualization in the same notebook.

Regards,  
Jan

---

<div class="post-metadata">

**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [February 24, 2021, 1:09pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/11 "2021-02-24T13:09:55Z")

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It appears `wxPython` has [wheels](https://pypi.org/project/wxPython/#files) available for macOS and Windows. Are you using either of these platforms?

If not, your system would have to build the python package from source which means you would have to have all the build dependencies. This is often problematic for users.

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**Author:** ![Jan\_Alexander](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jan_alexander/32/6831_2.png) [@Jan\_Alexander](https://discourse.slicer.org/u/Jan_Alexander)\
**Post date:** [February 25, 2021, 8:10am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/12 "2021-02-25T08:10:11Z")

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I am trying to accomplish this in the slicer notebook [docker](https://hub.docker.com/r/lassoan/slicer-notebook).

This docker image is debian linux based. This is why I try to install from `https://extras.wxpython.org/wxPython4/extras/linux/gtk3/debian-8`

Is there a better way?

Jan

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 25, 2021, 6:51pm UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/13 "2021-02-25T18:51:28Z")

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wxWidgets matplotlib backend is not usable from notebooks and it blocks the application’s event loop. You can try to use matplotlib with a notebook-friendly backend; or use other web-native visualization packages that can be used interactively in notebooks.

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<div class="post-metadata">

**Author:** ![Jan\_Alexander](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jan_alexander/32/6831_2.png) [@Jan\_Alexander](https://discourse.slicer.org/u/Jan_Alexander)\
**Post date:** [March 1, 2021, 11:12am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/14 "2021-03-01T11:12:10Z")

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Thank you, I was able to get it working eventually with

`slicernb.MatplotlibDisplay(matplotlib.pyplot)`

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<div class="post-metadata">

**Author:** ![Xiaojie\_Guo](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/xiaojie_guo/32/67098_2.png) [@Xiaojie\_Guo](https://discourse.slicer.org/u/Xiaojie_Guo)\
**Post date:** [December 13, 2024, 3:44am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/15 "2024-12-13T03:44:40Z")

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Hi, @lassoan. Recently, I have become interested in the PythonSlicer project. I have built Slicer-5.6.2 on Win10. What interests me is how to build PythonSlicer.exe in the Slicer project. The project is generated by CMake and opened using Visual Studio. I searched for PythonSlicer as a keyword but couldn’t find this project. It seems that there is not a project called PythonSlicer, but there are some projects related to Python. I don’t know what they mean. So my question is how do I find the project which built the PythonSlicer.exe? I want to learn how to build PythonSlicer. So I can use a similar method in my project.

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [December 13, 2024, 4:56am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/16 "2024-12-13T04:56:22Z")

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`PythonSlicer` is a launcher: a small application that sets up the runtime environment (mostly for loading dynamic libraries from various folders) and launches the Python interpreter (`Python-real`). The launcher is prebuilt, because Qt libraries needs to be linked statically in the launcher, which requires commercial license. The launcher executable is created by downloading and renaming the prebuilt launcher application.

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<div class="post-metadata">

**Author:** ![Xiaojie\_Guo](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/xiaojie_guo/32/67098_2.png) [@Xiaojie\_Guo](https://discourse.slicer.org/u/Xiaojie_Guo)\
**Post date:** [December 13, 2024, 6:00am UTC](https://discourse.slicer.org/t/use-full-power-of-python-in-slicer/7162/17 "2024-12-13T06:00:21Z")

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Thanks. I found that’s CTKAPPLauncher, right?