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Commit 1770b862 authored by Lanka Naga Sai Deep's avatar Lanka Naga Sai Deep
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%% Cell type:code id: tags:
``` python
import csv
import os
import sys
import numpy as np
import SimpleITK as sitk
from scipy.ndimage import zoom
```
%% Cell type:code id: tags:
``` python
def readMhd(filename):
print(filename)
# read mhd/raw image
itkimage = sitk.ReadImage(filename)
scan = sitk.GetArrayFromImage(itkimage) #3D image
spacing = itkimage.GetSpacing() #voxelsize
origin = itkimage.GetOrigin() #world coordinates of origin
transfmat = itkimage.GetDirection() #3D rotation matrix
return scan,spacing,origin,transfmat
```
%% Cell type:code id: tags:
``` python
[scan,spacing,origin,transfmat] = readMhd('D:\Lung cancer LNDb project\dataset\data\LNDb-0001.mhd')
[mask,spacing,origin,transfmat] = readMhd('D:\Lung cancer LNDb project\dataset\masks\LNDb-0001_rad1.mhd')
```
%% Output
D:\Lung cancer LNDb project\dataset\data\LNDb-0001.mhd
D:\Lung cancer LNDb project\dataset\masks\LNDb-0001_rad1.mhd
%% Cell type:code id: tags:
``` python
def getImgWorldTransfMats(spacing,transfmat):
# calc image to world to image transformation matrixes
transfmat = np.array([transfmat[0:3],transfmat[3:6],transfmat[6:9]])
for d in range(3):
transfmat[0:3,d] = transfmat[0:3,d]*spacing[d]
transfmat_toworld = transfmat #image to world coordinates conversion matrix
transfmat_toimg = np.linalg.inv(transfmat) #world to image coordinates conversion matrix
return transfmat_toimg,transfmat_toworld
```
%% Cell type:code id: tags:
``` python
def convertToImgCoord(xyz,origin,transfmat_toimg):
# convert world to image coordinates
xyz = xyz - origin
xyz = np.round(np.matmul(transfmat_toimg,xyz))
return xyz
```
%% Cell type:code id: tags:
``` python
transfmat_toimg,transfmat_toworld = getImgWorldTransfMats(spacing,transfmat)
```
%% Cell type:code id: tags:
``` python
ctr = np.array([-44.60839844,-119.0732422,-37.5])
ctr = convertToImgCoord(ctr,origin,transfmat_toimg)
ctr
```
%% Output
array([187., 313., 260.])
%% Cell type:code id: tags:
``` python
np.max(mask[0][0])==0
```
%% Output
True
%% Cell type:code id: tags:
``` python
mx = []
my = []
mz = []
for x in range(328):
if(np.max(mask[x])==0):
continue
for y in range(512):
if(np.max(mask[x][y])==0):
continue
for z in range(512):
if(mask[x][y][z]!=0):
mx.append(x)
my.append(y)
mz.append(z)
```
%% Output
[249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 249, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 251, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 252, 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%% Cell type:code id: tags:
``` python
print(min(mx),max(mx),min(my),max(my),min(mz),max(mz))
```
%% Output
249 263 294 325 172 312
%% Cell type:code id: tags:
``` python
sagital_image = scan[256, :, :] # Axis 0
mask_sagital_image = mask[256,:,:]
```
%% Cell type:code id: tags:
``` python
axial_image = scan[:, :, 242] # Axis 2
mask_axial_image = mask[:,:,242]
```
%% Cell type:code id: tags:
``` python
coronal_image = scan[:, 310, :] # Axis 1
mask_coronal_image = mask[:,310,:]
```
%% Cell type:code id: tags:
``` python
from matplotlib import pyplot as plt
```
%% Cell type:code id: tags:
``` python
fig, axs = plt.subplots(3,2)
axs[0][0].imshow(sagital_image)
axs[0][1].imshow(mask_sagital_image)
axs[1][0].imshow(axial_image)
axs[1][1].imshow(mask_axial_image)
axs[2][0].imshow(coronal_image)
axs[2][1].imshow(mask_coronal_image)
plt.savefig()
```
%% Output
%% Cell type:code id: tags:
``` python
scan1 = 255*((scan - np.min(scan))/(np.max(scan)-np.min(scan)))
```
%% Cell type:code id: tags:
``` python
sagital_image1 = scan1[0, :, :] # Axis 0
```
%% Cell type:code id: tags:
``` python
fig, axs = plt.subplots(1,2)
axs[0].imshow(sagital_image)
axs[1].imshow(sagital_image1)
plt.show()
```
%% Output
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-22-4e149890e5bd> in <module>
1 fig, axs = plt.subplots(1,2)
----> 2 axs[0].imshow(sagital_image)
3 axs[1].imshow(sagital_image1)
4 plt.show()
NameError: name 'sagital_image' is not defined
%% Cell type:code id: tags:
``` python
x = []
y = []
z = []
color = []
for i in range(249,264):
for j in range(294,326):
for k in range(172,313):
if(mask[i][j][k]>0):
x.append(i)
y.append(j)
z.append(k)
color.append(mask[i][j][k])
```
%% Cell type:code id: tags:
``` python
len(x)
```
%% Output
1608
%% Cell type:code id: tags:
``` python
%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits import mplot3d
fig = plt.figure()
ax = plt.axes(projection='3d')
ax.scatter3D(x, y, z, c=color)
```
%% Output
<mpl_toolkits.mplot3d.art3d.Path3DCollection at 0x18c82ab1c48>
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