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Commit 67c59e0989316f14d435beba41752315476960d3

Authored by Paulo Henrique Junqueira Amorim
1 parent 8e0e3fda
Exists in master and in 28 other branches canvas_reeng, canvas_text, casmoothing_cython, command-line, debian_cython, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, get_pixel, import_mesh, manual_v3.1, measure_canvas, measure_improvements, measure_placement_test, phoenix, region_growing_confidence, remove_local_wxpython, rmatsuda-fix_ref_MTC, rmatsuda-fix_remove_marker_bug, rmatsuda-trigger_bug_fix, segmentation_menu, select_part, smoothing_bin, smoothing_bin_pll, user_guide_en, xmartlabs-command-line

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README.md
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... ... @@ -18,64 +18,66 @@ InVesalius generates 3D medical imaging reconstructions based on a sequence of 2
18 18  
19 19 #### Linux 64 bits (tested on Ubuntu 16.04)
20 20  
21   -`sudo apt-get install python-wxgtk3.0 python-numpy python-scipy python-pil python-matplotlib python-skimage python-nibabel python-serial python-psutil python-vtk6 python-vtkgdcm python-gdcm python-casmoothing cython`
  21 +1) Install the packages: `sudo apt-get install python-wxgtk3.0 python-numpy python-scipy python-pil python-matplotlib python-skimage python-nibabel python-serial python-psutil python-vtk6 python-vtkgdcm python-gdcm python-casmoothing cython`
  22 +
  23 +2) Entrer InVesalius folder and execute: `python setup.py build_ext --inplace`
22 24  
23 25 #### Windows 64 bits (tested on Windows 7)
24 26  
25 27 1) **Python 2.7.8** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/python-2.7.8.amd64.msi
26 28  
27   -* Create a system variable named *%PYTHONPATH%* with values: *C:\Python27;C:\Python27\Lib;C:\Python27\Lib\site-packages;C:\Python27\Scripts;*
28   -* Insert into *Path* varibale the value *%PYTHONPATH%*
  29 +* Create a system variable named `%PYTHONPATH%` with values: `C:\Python27;C:\Python27\Lib;C:\Python27\Lib\site-packages;C:\Python27\Scripts;`
  30 +* Insert into `Path` varibale the value `%PYTHONPATH%`
29 31  
30 32 2) **wxPython 3.0.2** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/wxPython3.0-win64-3.0.2.0-py27.exe
31 33  
32 34 3) **PIP** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/get-pip.py
33   -* Download the script and execute *python get-pip.py*
  35 +* Download the script and execute `python get-pip.py`
34 36  
35 37 4) **Numpy 1.11.0** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/numpy-1.11.0+mkl-cp27-cp27m-win_amd64.whl
36   -* Download and execute *pip install numpy-1.11.0+mkl-cp27-cp27m-win_amd64.whl*
  38 +* Download and execute `pip install numpy-1.11.0+mkl-cp27-cp27m-win_amd64.whl`
37 39  
38 40 5) **Scipy 0.17.1** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/scipy-0.17.1-cp27-cp27m-win_amd64.whl
39   -* Download and execute *pip install scipy-0.17.1-cp27-cp27m-win_amd64.whl*
  41 +* Download and execute `pip install scipy-0.17.1-cp27-cp27m-win_amd64.whl`
40 42  
41 43 6) **Pillow (new Python Image Library)** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/Pillow-3.2.0-cp27-cp27m-win_amd64.whl
42   -* Download and execute *pip install Pillow-3.2.0-cp27-cp27m-win_amd64.whl*
  44 +* Download and execute `pip install Pillow-3.2.0-cp27-cp27m-win_amd64.whl`
43 45  
44 46 7) **Matplotlib 1.5.1** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/matplotlib-1.5.1-cp27-none-win_amd64.whl
45   -* Download and execute *pip install matplotlib-1.5.1-cp27-none-win_amd64.whl*
  47 +* Download and execute `pip install matplotlib-1.5.1-cp27-none-win_amd64.whl`
46 48  
47 49 8) **Scikit Image 0.12.3** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/scikit_image-0.12.3-cp27-cp27m-win_amd64.whl
48   -* Download and execute *pip install scikit_image-0.12.3-cp27-cp27m-win_amd64.whl*
  50 +* Download and execute `pip install scikit_image-0.12.3-cp27-cp27m-win_amd64.whl`
49 51  
50 52 9) **Nibabel 2.0.2** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/nibabel-2.0.2-py2.py3-none-any.whl
51   -* Download and execute *pip install nibabel-2.0.2-py2.py3-none-any.whl*
  53 +* Download and execute `pip install nibabel-2.0.2-py2.py3-none-any.whl`
52 54  
53 55 10) **PySerial 3.0.1** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/pyserial-3.0.1-py2.py3-none-any.whl
54   -* Download and execute *pip install pyserial-3.0.1-py2.py3-none-any.whl*
  56 +* Download and execute `pip install pyserial-3.0.1-py2.py3-none-any.whl`
55 57  
56 58 11) **PSUtil 4.2.0** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/psutil-4.2.0-cp27-cp27m-win_amd64.whl
57   -* Download and execute *pip install psutil-4.2.0-cp27-cp27m-win_amd64.whl*
  59 +* Download and execute `pip install psutil-4.2.0-cp27-cp27m-win_amd64.whl`
58 60  
59 61 12) **VTK 6.3.0** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/vtk.zip
60   -* Download and unzip on *C:\Python27\Lib\site-packages* and add on *%PYTHONPATH%* variable the value *C:\Python27\Lib\site-packages\vtk\vtk;*
  62 +* Download and unzip on `C:\Python27\Lib\site-packages` and add on `%PYTHONPATH%` variable the value `C:\Python27\Lib\site-packages\vtk\vtk;`
61 63  
62 64 13) **GDCM (trunk)** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/gdcm.zip
63   -* Download and unzip on *C:\Python27\Lib\site-packages* and add on *%PYTHONPATH%* variable the value *C:\Python27\Lib\site-packages\gdcm;*
  65 +* Download and unzip on `C:\Python27\Lib\site-packages` and add on `%PYTHONPATH%` variable the value `C:\Python27\Lib\site-packages\gdcm;`
64 66  
65 67 14) **CA Smoothing** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/python_ca_smoothing.zip
66   -* Download and unzip the two files on *C:\Python27\Lib\site-packages*
  68 +* Download and unzip the two files on `C:\Python27\Lib\site-packages`
67 69  
68 70 15) **Visual C++ 2015 Runtime** - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/vcredist_x64.exe
69 71 * Download and install
70 72  
71 73 16) **Cython**
72   -* Execute *python install cython*
  74 +* Execute `python install cython`
73 75  
74 76 17) **Compiled InVesalius parts**
75 77  
76   -* Option 1: Install [Microsoft Visual Studio Community 2015](https://www.visualstudio.com/pt-br/downloads/download-visual-studio-vs.aspx) and execute *python setup.py build_ext --inplace* on invesalius3 folder.
  78 +* Option 1: Install [Microsoft Visual Studio Community 2015](https://www.visualstudio.com/pt-br/downloads/download-visual-studio-vs.aspx) and execute `python setup.py build_ext --inplace` on invesalius3 folder.
77 79  
78   -* Option 2: Download compiled parts and unzip on *invesalius3/invesalius/data* - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/invesalius-compiled_parts.zip
  80 +* Option 2: Download compiled parts and unzip on `invesalius3/invesalius/data` - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/invesalius-compiled_parts.zip
79 81  
80 82  
81 83 Special thank's to Christoph Gohlke, Laboratory for Fluorescence Dynamics, University of California, Irvine for providing the pre-compiled of various [python packages for Windows 64 bits](http://www.lfd.uci.edu/~gohlke/pythonlibs/)
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