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3D medical imaging reconstruction software

License: GNU General Public License v2.0

Python 97.40% Dockerfile 0.03% Cython 2.57%

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paulojamorim tfmoraes vhosouza ruppert rubenkar raonyguimaraes rogeriofalcone vinodtakarkhede dragonlet eraleman guiandmag andersonbrayner yangwao biomaglab ruanaragao virajshah swordist dfelinto givanaldo freesciencecommunity vicself lynch829 151706061 peresasc saectar houssk victorgabr daniellemccool sketchbytes fellipeesteves swayfreeda lisandro11 foreverdavid volodymyr-syvochka top501 nagyistge wgui1 scholltan doutianbao ffsouza rmatsuda fabio-otsuka aomiit bryant1410 xmartlabs zyzzyva-c rics-ucsp laurestk yuxuanluo cesarconterno dolphinking hmaya enginbozkurt rsisto peterzhousz upaternostro zhanghelook 555learnwithme555 mtal3t baifengbai banupluie nneerr123 lscoder stoensin zhaoqiangshen otaviocarlos mokuzaru jaggzh zdpdev abelaarao shihao80 jmoreno555 vicdaar r0xen xiazt mahdiramadhan sajidullah l1uchao jackusa medical-images-process djson hiyanglian darkberg captain-xf augmen luzhongtong ddbxyrj devhliu loveplay1983 amirsalah backswimming sskram iiat-mr-xww nobbie2009 sparklerl luochengleo salialavi todun albertfjcostaifam jercylew

invesalius3's Issues

Error compiling Cython file

Hi guys.

I'm trying to compile InVesalius on Linux Ubuntu 13.10. When the digit following command:

$ [sudo] python setup.py install

I have this error message in Terminal:

will be a problem in the version of Cython?

Improvement on markers for navigation

What if there are several markers with the same fiducials labels? The last ones are chosen, but user must know that. This is an issue because when user select wrong fiducials and then correct them, there will always be multiple fiducials markers in list control.
Highlight the marker in volume viewer that is currently selected to be deleted or ID edited in list control. Create an arrow to show? Blink? Change color or increase size?
When you click fast and several times in create marker during navigation, it takes long to update the list control with the coordinates. Check this.

Display all DICOM tags information

A window to list all DICOM information tags.

Polhemus connect/disconnect issue

You can connect only once with a Polhemus tracking device. It does not disconnect propoerly if you change the tracking device or disconnect the current. Then it is necessary to restart InVesalius and the Polhemus device to make things work again.

Surface transparency slider inverted value order

Surface transparency slider value start with surface value all transparent but model is visible (correct). Invert slider value when started.

Inversão Lado Lesão Invesalius 3.0 final

Gostaria de informar-lhes que detectamos um erro no Invesalius na hora de abrir os arquivos Dicom de uma tomografia. A lesão do paciente se encontra no lado esquerdo do crânio e ao processar a tomografia o modelo 3D gerado pelo invesalius aparece do lado direito.

Gostaria de saber se existe alguma forma de ver porque esse problema está acontecendo

Obrigado

Create option to save log file

Option to enable or disable log file

Save the following items:

Date and time of each event
Information about each interaction, button click, open menu etc.
Volume and image interation
Unexpected and expected exceptions and errors

Export InVesalius mobile format

Export PGM format to InVesalius mobile.

Error start python invesalius.py

Hey guys.

I'm with problem in comand python invesalius.py.

Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_misc.py", line 1358, in Notify
self.notify()
File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/core.py", line 14767, in Notify
self.result = self.callable(self.args, *self.kwargs)
File "invesalius.py", line 174, in Startup
from gui.frame import Frame
File "/home/brenopolanski/Desktop/SVN/invesalius3-3.0-b5/invesalius/gui/frame.py", line 31, in
import default_tasks as tasks
File "/home/brenopolanski/Desktop/SVN/invesalius3-3.0-b5/invesalius/gui/default_tasks.py", line 25, in
import data_notebook as nb
File "/home/brenopolanski/Desktop/SVN/invesalius3-3.0-b5/invesalius/gui/data_notebook.py", line 36, in
import data.slice as slice
File "/home/brenopolanski/Desktop/SVN/invesalius3-3.0-b5/invesalius/data/slice.py", line 36, in
from data import mips
ImportError: cannot import name mips
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_misc.py", line 1358, in Notify
self.notify()
File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 14767, in Notify
self.result = self.callable(_self.args, *_self.kwargs)
File "invesalius.py", line 82, in Startup2
self.control = self.splash.control
AttributeError: 'SplashScreen' object has no attribute 'control'
Traceback (most recent call last):
File "invesalius.py", line 197, in OnClose
if self.fc.IsRunning():
AttributeError: 'SplashScreen' object has no attribute 'fc'

Surface part selection

Enhancement usability surface part selection. When select null parts InVesalius is crashed.

Create option to list DICOM files without re-load

Create an option to return to the import screen, list the series without import a folder.

Suggestion: Dr. Romero Antunes Barreto Lins

Compiling cy_mesh

Following the instructions in INSTALL file and running:

python setup.py install

All files are compiled but no cy_mesh.pyd is created. This avoid running invesalius as it raises an error that could not import cy_mesh.

However, when running:

python setup.py build_ext --inplace

it creates the cy_mesh.pyd.
Need to fix this compilation bug while configuring invesalius.

Image filter tool

Add tool for filter images. Ex. despeckle, border detection etc.

bug: surfaces list pile up

When a project is opened and then closed, the surfaces list pile up with the next opened project's surfaces.

Report tool

Add tool to make report about case.

May be insert basic DICOM information in header
Insert measures
Insert screenshot
Template possibility

Update language list

Measure density tool

Region growing

Implement region growing in masks.

Change measures position from 3D and 2D

Linear "curved" measurement in surface

Add linear measurement that accompanies the surface.

Error while building invesalius in Windows 8.1 x64

Hi,
I followed the article https://github.com/invesalius/invesalius3/wiki/Running-InVesalius-3-in-Windows to build invesalius in Windows 8.1 64bit 4GB RAM with Visual Studio Professional 2015 installed and got the following error when i ran python setup.py build_ext --inplace
Cython 0.24.1 was installed in my system. Please help me solve this problem

Error compiling Cython file:
------------------------------------------------------------
...
]

@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline double interpolate(image_t[:, :, :] V, double x, double y, double z)
 nogil:
                              ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:80:31: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...


@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
           ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:126:12: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...


@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
                      ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:126:23: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...


@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef void calc_coef_tricub(image_t[:, :, :] V, double x, double y, double z, dou
ble [64] coef) nogil:
                          ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:153:27: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...


@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline double tricub_interpolate(image_t[:, :, :] V, double x, double y, do
uble z) nogil:
                                     ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:239:38: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...


@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline double tricubicInterpolate(image_t[:, :, :] V, double x, double y, d
ouble z) nogil:
                                      ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:283:39: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
    arr[2] = bicubicInterpolate(p[2], y-yi, z-zi)
    arr[3] = bicubicInterpolate(p[3], y-yi, z-zi)
    return cubicInterpolate(arr, x-xi)


def tricub_interpolate_py(image_t[:, :, :] V, double x, double y, double z):
                         ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:306:26: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...


def tricub_interpolate_py(image_t[:, :, :] V, double x, double y, double z):
    return tricub_interpolate(V, x, y, z)

def tricub_interpolate2_py(image_t[:, :, :] V, double x, double y, double z):
                          ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:309:27: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
    return tricub_interpolate(V, x, y, z)

def tricub_interpolate2_py(image_t[:, :, :] V, double x, double y, double z):
    return tricubicInterpolate(V, x, y, z)

def trilin_interpolate_py(image_t[:, :, :] V, double x, double y, double z):
                         ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:312:26: 'image_t' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
                   ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:128:20: Coercion from Python not allowed witho
ut the GIL

Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
                   ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:128:20: Calling gil-requiring function not all
owed without gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
               ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:128:16: Indexing Python object not allowed wit
hout gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False) # turn of bounds-checking for entire function
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
         ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:128:10: Accessing Python attribute not allowed
 without gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
                   ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:129:20: Coercion from Python not allowed witho
ut the GIL

Error compiling Cython file:
------------------------------------------------------------
...
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
                   ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:129:20: Calling gil-requiring function not all
owed without gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
               ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:129:16: Indexing Python object not allowed wit
hout gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.cdivision(True)
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
         ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:129:10: Accessing Python attribute not allowed
 without gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
    dx = V.shape[2] - 1
                   ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:130:20: Coercion from Python not allowed witho
ut the GIL

Error compiling Cython file:
------------------------------------------------------------
...
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
    dx = V.shape[2] - 1
                   ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:130:20: Calling gil-requiring function not all
owed without gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
    dx = V.shape[2] - 1
               ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:130:16: Indexing Python object not allowed wit
hout gil

Error compiling Cython file:
------------------------------------------------------------
...
@cython.wraparound(False)
cdef inline image_t _G(image_t[:, :, :] V, int x, int y, int z) nogil:
    cdef int dz, dy, dx
    dz = V.shape[0] - 1
    dy = V.shape[1] - 1
    dx = V.shape[2] - 1
         ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:130:10: Accessing Python attribute not allowed
 without gil

Error compiling Cython file:
------------------------------------------------------------
...
    if z <  0:
        z = dz + z + 1
    elif z > dz:
        z = z - dz - 1

    return V[z, y, x]
           ^
------------------------------------------------------------

invesalius\data\interpolation.pyx:147:12: Constructing Python tuple not allowed
without gil
Traceback (most recent call last):
  File "setup.py", line 44, in <module>
    extra_compile_args=['/openmp'],),
  File "C:\Python27\Lib\site-packages\Cython\Build\Dependencies.py", line 915, i
n cythonize
    cythonize_one(*args)
  File "C:\Python27\Lib\site-packages\Cython\Build\Dependencies.py", line 1037,
in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: invesalius/data/interpolation.pyx

Disable two clicks (reset) when image editor is activated

The problem is when you are editing quickly and it make two click, the view is reseted.

Reported by Alberto Cabús Junior

Undo and Redo

Finalize undo and redo implementation.

PACS support

Perform DICOM import files from PACS server

DICOM tag edit and anonymize tool

Edit tag option
Export anonymized DICOM

Capture video of screen

Capture video of screen
Option for export video of volume/surface rotating with
Insert InVesalius logo

Image register tool

Add image register tool

Volume Raycasting - Color presets

Insert color presets option in volume raycasting

DICOM-support, general use is possible?

Can I adapt DICOM-support for general use for open and convert medical data and images?

Display dialog on save surface and project dialog

Display a window while surface or project is save.

InVesalius 3.1.0 installed on windows10 cannot open

Reorient image tool not work after open project

Traceback (most recent call last): File "/invesalius3/invesalius/data/styles.py", line 1553, in OnMouseMove self._rotate() File "/invesalius3/invesalius/data/styles.py", line 1654, in _rotate self.viewer.slice_.current_mask.clear_history() AttributeError: 'NoneType' object has no attribute 'clear_history'

Invesalius request me to provide more than one DICOM file for 3D reconstruction.

Hi, i have one .dcm file and Invesalius cant do a reconstruction, but i can open the file in de programs Blueskybio and Osirix and i can see the 3D reconstruction. What can i do?.

Ruler/scale in viewer 2D/3D

Add ruler/scale in viewer 2D/3D
Add option to enable/disable ruler

Image edition tool: square not work

Square of image edition tool not working.

Region of Interest - ROI

Implement region of interest tool for masks.

Surface generation options is shown if image is reoriented

To reproduce:

1 - Reorient image
2 - Click on create surface

Note: The mask was not edited for this.

Volume rendering cut/remove parts

Add volume rendering cut/remove parts tool

Update manual

Web version?

There are a "web version" plan, fork or working group?

DICOM multiframe support

Insert support for DICOM multiframe (see: ftp://dicom.nema.org/MEDICAL/dicom/2014c/output/chtml/part03/sect_C.7.6.6.html)

Not closing InVesalius when in reorientation style

High DPI display support

On high DPI display (DPI>200) some widgets and text are not shown correctly which make some function not quite usable. Especially the left panel.

Multiplanar visualization fails to update automatically

InVeslius master branch in Windows 10, Python 2.7 and wxPython 3.
After importing a DICOM folder and generating a multiplanar visualization the window fails to update automatically, see figure below. To update main frame is necessary to "move" the window.

loading dicom files

when i open the software and try to import dicom files . this dialod box appears and nothing happens.

please guide me

Inverted orientation when opening a coronal case

The promed case 2571 coronal serie is inverted in right-left orientation.

UserWarning: failed to import module _transformations （win8.1）

Hello,
I just follow " Running-InVesalius-3-in-Windows "; when I run app.py , it show:
Warning (from warnings module):
File "E:\InVesalius\python27\Lib\site-packages\invesalius3-master\invesalius\data\transformations.py", line 1899
warnings.warn("failed to import module %s" % name)
UserWarning: failed to import module _transformations

although I can use "invesalius",I want to know how to solve this warning

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