diff --git a/AmpScan/AmpScanGUI.py b/AmpScan/AmpScanGUI.py
index 38b6f52a307d2e8c9064a4b26c4175d1b5eac129..80dd68e87ac164e5e78b7d8eb5714134ef80cace 100644
--- a/AmpScan/AmpScanGUI.py
+++ b/AmpScan/AmpScanGUI.py
@@ -18,6 +18,7 @@ class AmpScanGUI(QMainWindow):
def __init__(self, parent = None):
super(AmpScanGUI, self).__init__()
self.vtkWidget = qtVtkWindow()
+ self.renWin = self.vtkWidget._RenderWindow
self.mainWidget = QWidget()
self.AmpObj = None
# self.CMap = np.array([[212.0, 221.0, 225.0],
@@ -36,13 +37,13 @@ class AmpScanGUI(QMainWindow):
self.fname = QFileDialog.getOpenFileName(self, 'Open file',
filter="Meshes (*.stl)")
if self.AmpObj is not None:
- self.vtkWidget.renderActors(self.AmpObj.actors, [])
+ self.renWin.renderActors(self.AmpObj.actors, [])
self.AmpObj = AmpObject(self.fname[0], 'limb')
self.AmpObj.addActor(stype='limb')
self.AmpObj.lp_smooth(stype='limb')
- self.vtkWidget.setnumViewports(1)
- self.vtkWidget.setProjection()
- self.vtkWidget.renderActors(self.AmpObj.actors, ['limb',])
+ self.renWin.setnumViewports(1)
+ self.renWin.setProjection()
+ self.renWin.renderActors(self.AmpObj.actors, ['limb',])
def chooseSocket(self):
self.sockfname = QFileDialog.getOpenFileName(self, 'Open file',
@@ -52,17 +53,17 @@ class AmpScanGUI(QMainWindow):
self.AmpObj.lp_smooth(stype='socket')
def align(self):
- self.vtkWidget.setnumViewports(2)
- self.vtkWidget.setView(view=[-1, 0, 0], viewport=1)
- self.vtkWidget.setProjection(True, 0)
- self.vtkWidget.setProjection(True, 1)
-# self.vtkWidget.render(self.AmpObj.actors, dispActors=['limb',])
-# self.vtkWidget.render(self.AmpObj.actors, dispActors=['socket',],
+ self.renWin.setnumViewports(2)
+ self.renWin.setView(view=[-1, 0, 0], viewport=1)
+ self.renWin.setProjection(True, 0)
+ self.renWin.setProjection(True, 1)
+# self.renWin.render(self.AmpObj.actors, dispActors=['limb',])
+# self.renWin.render(self.AmpObj.actors, dispActors=['socket',],
# viewport=1)
- self.vtkWidget.renderActors(self.AmpObj.actors,
+ self.renWin.renderActors(self.AmpObj.actors,
dispActors=['limb', 'socket'],
viewport=0)
- self.vtkWidget.renderActors(self.AmpObj.actors,
+ self.renWin.renderActors(self.AmpObj.actors,
dispActors=['limb', 'socket'],
viewport=1)
self.AmpObj.actors['limb'].setColor([1.0, 0.0, 0.0])
@@ -71,14 +72,14 @@ class AmpScanGUI(QMainWindow):
self.AmpObj.actors['socket'].setOpacity(0.5)
def register(self):
- self.vtkWidget.setnumViewports(1)
- self.vtkWidget.setProjection()
+ self.renWin.setnumViewports(1)
+ self.renWin.setProjection()
self.RegObj = regObject(self.AmpObj)
self.RegObj.registration(steps=5, baseline='socket', target='limb',
reg = 'reglimb', direct=True)
self.RegObj.addActor(stype='reglimb', CMap=self.AmpObj.CMapN2P)
- self.vtkWidget.renderActors(self.AmpObj.actors, ['reglimb',], shading=False)
- self.vtkWidget.setScalarBar(self.AmpObj.actors['reglimb'])
+ self.renWin.renderActors(self.AmpObj.actors, ['reglimb',], shading=False)
+ self.renWin.setScalarBar(self.AmpObj.actors['reglimb'])
def analyse(self):
self.RegObj.plot_slices()
@@ -86,20 +87,20 @@ class AmpScanGUI(QMainWindow):
def chooseFE(self):
FEname = QFileDialog.getOpenFileName(self, 'Open file',
filter="FE results (*.npy)")
- self.vtkWidget.setnumViewports(1)
+ self.renWin.setnumViewports(1)
self.AmpObj.addFE([FEname[0],])
self.AmpObj.lp_smooth('FE', n=1)
self.AmpObj.addActor(stype='FE', CMap=self.AmpObj.CMap02P, bands=5)
self.AmpObj.actors['FE'].setScalarRange(smin=0.0, smax=50)
- self.vtkWidget.renderActors(self.AmpObj.actors, ['FE',], shading=True)
- self.vtkWidget.setScalarBar(self.AmpObj.actors['FE'])
+ self.renWin.renderActors(self.AmpObj.actors, ['FE',], shading=True)
+ self.renWin.setScalarBar(self.AmpObj.actors['FE'])
def choosePress(self):
vName = QFileDialog.getOpenFileName(self, 'Open file',
filter="Sensor vertices (*.csv)")
pName = QFileDialog.getOpenFileName(self, 'Open file',
filter="Sensor pressures (*.csv)")
- self.vtkWidget.setnumViewports(1)
+ self.renWin.setnumViewports(1)
self.pSense = pressSense()
self.pSense.calcFaces(d=5)
self.pSense.importVert(vName[0])
@@ -108,8 +109,8 @@ class AmpScanGUI(QMainWindow):
self.AmpObj.actors['antS'] = self.pSense.actors['antS']
self.AmpObj.actors['socket'].setColor([1.0, 1.0, 1.0])
self.AmpObj.actors['socket'].setOpacity(1.0)
- self.vtkWidget.renderActors(self.AmpObj.actors, ['socket', 'antS'])
- self.vtkWidget.setScalarBar(self.AmpObj.actors['antS'])
+ self.renWin.renderActors(self.AmpObj.actors, ['socket', 'antS'])
+ self.renWin.setScalarBar(self.AmpObj.actors['antS'])
def createActions(self):
self.openFile = QAction(QIcon('open.png'), 'Open', self,
diff --git a/AmpScan/ampVis.py b/AmpScan/ampVis.py
index 57d38daf1acc454983058196cfedf6ae4a097784..165d848f15ae476e765e093efd10923bd4352024 100644
--- a/AmpScan/ampVis.py
+++ b/AmpScan/ampVis.py
@@ -5,13 +5,14 @@ Created on Thu Sep 28 13:19:18 2017
@author: js22g12
Functions that deal with the visualisation of the limb and data
+
+Includes interfaces to deal
"""
import numpy as np
import vtk
from vtk.util import numpy_support
from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
-from PyQt5.QtWidgets import QWidget
class vtkRender(vtk.vtkRenderer):
"""
@@ -69,18 +70,23 @@ class ampVTK(object):
self.scalar_bar.SetPosition2(0.1, 0.3)
self.rens[0].AddActor(self.scalar_bar)
-
-
def setView(self, view = [0, -1, 0], viewport=0):
self.cams[viewport].SetPosition(view[0], view[1], view[2])
self.cams[viewport].SetViewUp(-0.0, 0.0, 1.0)
def setBackground(self, color=[0.1, 0.2, 0.4]):
+ """
+ Set the background colour of the renderer
+ """
for ren in self.rens:
ren.SetBackground(color)
def setProjection(self, perspective=False, viewport=0):
- self.cams[viewport].SetParallelProjection(perspective)
+ """
+ Set the projection of the camera to either parallel or perspective
+
+ """
+ self.cams[viewport].SetParallelProjection(perspective)
def addAxes(self, actors, viewport=0, color = [1.0, 1.0, 1.0], font=None):
@@ -109,55 +115,6 @@ class ampVTK(object):
# self.rens[viewport].AddActor(self.axes[viewport])
-class qtVtkWindow(QVTKRenderWindowInteractor, ampVTK):
-
- def __init__(self):
- super(qtVtkWindow, self).__init__()
- self.SetInteractorStyle(self.style)
- self.GetRenderWindow().AddRenderer(self.rens[0])
- self.iren = self.GetRenderWindow().GetInteractor()
- self.iren.Initialize()
-
- def setnumViewports(self, n):
- """
- Function to set multiple viewports within the vtkWindow
-
- Parameters
- ------------
- n: int
- number of viewports required
- """
- dif = n - len(self.rens)
- if dif == 0:
- return
- elif dif < 0:
- for ren in self.rens[n:]:
- self.GetRenderWindow().RemoveRenderer(ren)
- self.rens = self.rens[:n]
- elif dif > 0:
- for i in range(dif):
- self.rens.append(vtkRender())
- self.axes.append(vtk.vtkCubeAxesActor())
- self.GetRenderWindow().AddRenderer(self.rens[-1])
- if len(self.cams) < len(self.rens):
- self.cams.append(vtk.vtkCamera())
- self.rens[-1].SetActiveCamera(self.cams[len(self.rens)-1])
- for i, ren in enumerate(self.rens):
- ren.SetViewport(float(i)/n, 0, float(i+1)/n, 1)
- self.setBackground()
-
-
-class vtkRenWin(vtk.vtkRenderWindow, ampVTK):
-
- def __init__(self, winWidth=512, winHeight=512):
- super(vtkRenWin, self).__init__()
- self.winWidth = winWidth
- self.winHeight = winHeight
- self.SetSize(self.winWidth, self.winHeight)
- self.OffScreenRenderingOn()
- self.AddRenderer(self.rens[0])
- self.Render()
-
def setnumViewports(self, n):
"""
Function to set multiple viewports within the vtkWindow
@@ -188,11 +145,11 @@ class vtkRenWin(vtk.vtkRenderWindow, ampVTK):
def getImage(self):
- self.vtkRGB = vtk.vtkUnsignedCharArray()
+ vtkRGB = vtk.vtkUnsignedCharArray()
self.GetPixelData(0, 0, self.winWidth-1, self.winHeight-1,
- 1, self.vtkRGB)
- self.vtkRGB.Squeeze()
- self.im = np.flipud(np.resize(np.array(self.vtkRGB),
+ 1, vtkRGB)
+ vtkRGB.Squeeze()
+ self.im = np.flipud(np.resize(np.array(vtkRGB),
[self.winWidth, self.winHeight, 3])) / 255.0
def getScreenshot(self, fname, mag=10):
@@ -209,17 +166,54 @@ class vtkRenWin(vtk.vtkRenderWindow, ampVTK):
writer.Write()
+class vtkRenWin(vtk.vtkRenderWindow, ampVTK):
+
+ def __init__(self, qt = True, winWidth=512, winHeight=512):
+ super(vtkRenWin, self).__init__()
+ self.AddRenderer(self.rens[0])
+ if qt is False:
+ self.winWidth = winWidth
+ self.winHeight = winHeight
+ self.SetSize(self.winWidth, self.winHeight)
+ self.OffScreenRenderingOn()
+ self.Render()
+
+
+class qtVtkWindow(QVTKRenderWindowInteractor):
+ """
+ Create a vtk window to be embeded within a qt GUI
+ Inherites the QVTKRenderWindowInteractor class and the
+
+ Fix issue with SetInteractorStyle
+ """
+
+ def __init__(self):
+ super(qtVtkWindow, self).__init__(rw=vtkRenWin())
+ #self.SetInteractorStyle(self.style)
+ self.iren = self._RenderWindow.GetInteractor()
+ self.iren.Initialize()
+
class visMixin(object):
+ """
+ Visualisation methods that act upon the AmpObj itself
+ Methods for generating the custom AmpObj actor to interface with vtk
+ """
def genIm(self, actor=['limb'], winWidth=512, winHeight=512,
views=[[0, -1, 0]], background=[1.0, 1.0, 1.0], projection=True,
shading=True, mag=10, out='im', name='test.tiff'):
"""
+ Output an image of an actor either as an array or a saved png file
+
"""
- win = vtkRenWin(winWidth, winHeight)
+ # Generate a renderer window
+ win = vtkRenWin(False, winWidth, winHeight)
+ # Set the number of viewports
win.setnumViewports(len(views))
+ # Set the background colour
win.setBackground(background)
+ # Set camera projection
win.setProjection(projection)
for i, view in enumerate(views):
win.addAxes(self.actors, color=[0.0, 0.0, 0.0], viewport=i)
@@ -227,8 +221,8 @@ class visMixin(object):
win.setProjection(projection, viewport=i)
win.renderActors(self.actors, actor, viewport=i, shading=shading, zoom=1.3)
win.Render()
- win.getImage()
if out == 'im':
+ win.getImage()
return win.im
elif out == 'fh':
win.getScreenshot(name)
@@ -252,8 +246,6 @@ class visMixin(object):
Class that inherits methods from vtk actor
Contains functions to set vertices, faces, scalars and color map
from numpy arrays
-
- Add functions to add vert, add faces, cmap and make LUT
"""
def __init__(self, data, CMap=None, bands=128):
diff --git a/AmpScan/core.py b/AmpScan/core.py
index 027a86dec54733a2dadcc52f45560f772baf777c..37c95ac3dba5f2b4536e5fcdd4666fae9f6f2ed8 100644
--- a/AmpScan/core.py
+++ b/AmpScan/core.py
@@ -6,8 +6,6 @@ Created on Wed Sep 13 13:54:23 2017
Core functions for the AmpObject
-Remove pd dependency and instead just use numpy arrays
-
Requires numpy 1.13
@@ -69,6 +67,14 @@ class AmpObject(alignMixin, trimMixin, smoothMixin, analyseMixin,
else:
raise ValueError('dtype not supported, please choose from ' +
'limb, socket, reglimb, regsocket, MRI or AmpObj')
+
+ def createCMap(self, cmap=None, n = 50):
+ """
+ Function to generate a colormap for the AmpObj
+ """
+ if cmap is None:
+ cmap = n
+
def addData(self, Data, stype):
@@ -177,6 +183,9 @@ class AmpObject(alignMixin, trimMixin, smoothMixin, analyseMixin,
data['faceEdges'][eF[~logic], 1] = fInd[~logic]
def vNorm(self, stype=0):
+ """
+ Function to compute the vertex normals
+ """
if isinstance(stype, int):
stype = self.stype[stype]
data = getattr(self, stype)
diff --git a/README.rst b/README.rst
deleted file mode 100644
index a4d653ee843ab92011c009c15d5dcdfb3f3078e4..0000000000000000000000000000000000000000
--- a/README.rst
+++ /dev/null
@@ -1,104 +0,0 @@
-AmpScan ReadME File
---------------------
-
-Author: Joshua Steer
-
-To install the package, open the cmd prompt and type the following script
-
-J:
-cd J:\Shared Resources\AmpScan IfLS Team\100 PYTHON\Code
-pip install .
-
-To use the package
-
- import AmpScan
- import os
-
- read_filename = '01_PhantomShell_ICEM_3mm.stl'
- write_filename = '01_PhantomShell_ICEM_3mm_write.stl'
-
- Data = AmpObject(target, 'limb')
- Data.addData(baseline, 'socket')
- Data.lp_smooth()
- Data.man_rot([5,5,5])
- Reg = regObject(Data)
- Reg.registration(steps=5, baseline='socket', target='limb', reg = 'reglimb')
- Reg.save(saveStr, stype='reglimb')
- Reg.plot_slices()
-
-
-
-Structure:
-
-AmpScan structure
-
-core.py
- class AmpObject(Data, stype)
- func addData
- func read_stl
- func unify_vertices
- func computeEdges
- func save
- func calc_norm
- func man_trans
- func man_rot
- func centre
-smooth.py
- class smoothMixin
- func lp_smooth
-autoAlign.py
- class alignMixin
- func icp
- func calcDistError
-trim.py
- class trimMixin
- func planarTrim
-analyse.py
- class analyseMixin
- func plot_slices
- func create_slice
- func planeEdgeIntersect
-ampVis.py
- class visMixin
- func genIm
- func addActor
- class ampActor
- func setVert
- func setFaces
- func setRect
- func setColor
- func setOpacity
- func setCMap
- class vtkRender
- class vtkWindow
- func render
- func setScalarBar
- func setViewports
- func addAxes
-registration.py
- class regObject
- func registration
-TSBSocketDesign.py
- class mplCanvas
- class dragSpline
- func connect
- func on_press
- func on_motion
- func on_release
- func disconnect
- func bezierCurve
-SocketDesignGUI.py
- class GUI
- func plotRect
- func chooseOpenFile
- func createActions
- func createMenus
-AmpScanGUI
- class GUI
- func chooseOpenFile
- func chooseSocket
- func align
- func register
- func analyse
- func createActions
- func createMenus