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LOTS_IM_GPU_lib.py
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LOTS_IM_GPU_lib.py
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from numba import cuda
import numpy as np
import math, numba, cv2
import os, random
import skimage.morphology as skimorph
import skimage.filters as skifilters
import matplotlib.pyplot as plt
import scipy.io as sio
from scipy import signal
import code
from timeit import default_timer as timer
## CUDA FUNCTIONS
@cuda.jit
def cu_sub_st(source, target, result):
si, ti = cuda.grid(2)
if si < source.shape[0] and ti < target.shape[0]:
for ii in range(0, result.shape[2]):
result[si,ti,ii] = source[si,ii] - target[ti,ii]
cuda.syncthreads()
@cuda.jit
def cu_sub_sqr_st(source, target, result):
si, ti = cuda.grid(2)
if si < source.shape[0] and ti < target.shape[0]:
for ii in range(0, result.shape[2]):
result[si,ti,ii] = (source[si,ii] - target[ti,ii]) * (source[si,ii] - target[ti,ii])
cuda.syncthreads()
@cuda.jit(device=True)
def cu_max_abs_1d(array):
temp = -9999
for i in range(0, array.shape[0]):
if array[i] > temp:
temp = array[i]
if temp < 0: temp *= -1
return temp
@cuda.jit(device=True)
def cu_mean_abs_1d(array):
temp = 0
for i in range(array.shape[0]):
temp += array[i]
if temp < 0: temp *= -1
return temp / array.size
@cuda.jit
def cu_max_mean_abs(inputs, results):
si, ti = cuda.grid(2)
if si < results.shape[0] and ti < results.shape[1]:
results[si,ti,0] = cu_max_abs_1d(inputs[si,ti,:])
results[si,ti,1] = cu_mean_abs_1d(inputs[si,ti,:])
cuda.syncthreads()
cuda.syncthreads()
@cuda.jit
def cu_distances(inputs, flag, outputs, alpha):
si, ti = cuda.grid(2)
if si < outputs.shape[0] and ti < outputs.shape[1]:
outputs[si,ti] = flag[si] * (alpha * inputs[si,ti,0] + (1 - alpha) * inputs[si,ti,1])
cuda.syncthreads()
cuda.syncthreads()
@cuda.jit
def cu_sort_distance(array):
i = cuda.grid(1)
if i < array.shape[0]:
for passnum in range(len(array[i,:]) - 1, 0, -1):
for j in range(passnum):
if array[i,j] > array[i,j + 1]:
temp = array[i,j]
array[i,j] = array[i,j + 1]
array[i,j + 1] = temp
cuda.syncthreads()
@cuda.jit
def cu_age_value(arrays, results):
i = cuda.grid(1)
if i < results.shape[0]:
results[i] = cu_mean_abs_1d(arrays[i,:])
cuda.syncthreads()
cuda.syncthreads()
## NON-CUDA FUNCTIONS
def set_mean_sample_number(num_samples_all):
'''
Set number of target patches used to calculate irregularity map.
'''
if num_samples_all == 64:
return 16
elif num_samples_all == 128:
return 32
elif num_samples_all == 256:
return 32
elif num_samples_all == 512:
return 64
elif num_samples_all == 1024:
return 128
elif num_samples_all == 2048:
return 256
else:
raise ValueError("Number of samples must be either 64, 128, 256, 512, 1024 or 2048!")
return 0
def gen_2d_source_target_patches(brain_slice, patch_size, num_samples, TRSH):
'''
Generate 2D source and target patches for LOTS-IM calculation
'''
[x_len, y_len] = brain_slice.shape
counter_y = int(y_len / patch_size) ## counter_y = 512 if patch of size 1 and image of size 512x512
counter_x = int(x_len / patch_size)
source_patch_len = counter_x * counter_y ## How many source patches are neede (e.g. for 1, we need one for each pixel)
mask_slice = np.nan_to_num(brain_slice)
mask_slice[mask_slice > 0] = 1
## Creating grid-patch 'xy-by-xy'
# -- Column
y_c = np.ceil(patch_size / 2)
y_c_sources = np.zeros(int(y_len / patch_size))
for iy in range(0, int(y_len / patch_size)):
y_c_sources[iy] = (iy * patch_size) + y_c - 1
# -- Row
x_c = np.ceil(patch_size / 2)
x_c_sources = np.zeros(int(x_len / patch_size))
for ix in range(0, int(x_len / patch_size)):
x_c_sources[ix] = (ix * patch_size) + x_c - 1
''' Extracting Source Patches '''
area_source_patch = np.zeros([1,patch_size,patch_size])
icv_source_flag = np.zeros([source_patch_len])
idx_mapping = np.ones([source_patch_len]) * -1
index = 0
idx_source= 0
if patch_size == 1:
area_source_patch = brain_slice[mask_slice == 1]
area_source_patch = area_source_patch.reshape([area_source_patch.shape[0], 1, 1])
index = source_patch_len
idx_source = area_source_patch.shape[0]
icv_source_flag = mask_slice.flatten()
positive_indices = (np.where(brain_slice.flatten() > 0))[0]
index = 0
for i in positive_indices:
idx_mapping[i] = index
index += 1
else:
area_source_patch = []
for isc in range(0, counter_x):
for jsc in range(0, counter_y):
icv_source_flag[index] = mask_slice[int(x_c_sources[isc]), int(y_c_sources[jsc])]
if icv_source_flag[index] == 1:
temp = get_area(x_c_sources[isc], y_c_sources[jsc],
patch_size, patch_size, brain_slice)
area_source_patch.append(temp.tolist())
idx_mapping[index] = idx_source
idx_source += 1
index += 1
area_source_patch = np.asarray(area_source_patch)
''' Extracting Target Patches '''
target_patches = []
index_debug = 0
random_array = np.random.randint(10, size=(x_len, y_len))
index_possible = np.zeros(brain_slice.shape)
index_possible[(mask_slice != 0) & (random_array > TRSH*10)] = 1
index_possible = np.argwhere(index_possible)
for index_chosen in index_possible:
x, y = index_chosen
area = get_area(x, y, patch_size, patch_size, brain_slice)
if area.size == patch_size * patch_size:
if np.random.randint(low=1, high=10)/10 < (100/(x*y)) * num_samples:
pass
target_patches.append(area)
index_debug += 1
target_patches_np = get_shuffled_patches(target_patches, num_samples)
target_patches_np = target_patches_np[0:num_samples,:,:]
print('Sampling finished: ' + ' with: ' + str(index_debug) + ' samples from: ' + str(x_len * y_len))
area = []
''''''
''' Reshaping array data for GPU (CUDA) calculation '''
source_patches_all = np.reshape(area_source_patch,(area_source_patch.shape[0],
area_source_patch.shape[1] * area_source_patch.shape[2]))
target_patches_all = np.reshape(target_patches_np, (target_patches_np.shape[0],
target_patches_np.shape[1] * target_patches_np.shape[2]))
return source_patches_all, target_patches_all, idx_source, idx_mapping
def gen_3d_source_target_patches(input_mri_data, patch_size, num_samples, thrsh_patches=None):
'''
Generate 3D source and target patches for LOTS-IM calculation
'''
## Get MRI measurements
[x_len, y_len, z_len] = input_mri_data.shape
whole_volume = x_len * y_len * z_len
## Create mask for whole brain
mri_mask = np.nan_to_num(input_mri_data)
mri_mask[mri_mask > 0] = 1
vol_slice = np.count_nonzero(input_mri_data) / whole_volume
print('DEBUG-Patch: brain - ' + str(np.count_nonzero(input_mri_data)) +
', x_len * y_len * z_len - ' + str(whole_volume) + ', vol: ' + str(round(vol_slice, 5)))
## Set the counter for each axis
counter_y = int(y_len / patch_size)
counter_x = int(x_len / patch_size)
counter_z = int(z_len / patch_size)
source_patch_len = counter_x * counter_y * counter_z
## Creating grid-patch 'x-by-y-by-z'
# -- Column
y_c = np.ceil(patch_size / 2)
y_c_sources = np.zeros(int(y_len / patch_size))
for iy in range(0, int(y_len / patch_size)):
y_c_sources[iy] = (iy * patch_size) + y_c - 1
# -- Row
x_c = np.ceil(patch_size / 2)
x_c_sources = np.zeros(int(x_len / patch_size))
for ix in range(0, int(x_len / patch_size)):
x_c_sources[ix] = (ix * patch_size) + x_c - 1
# -- Depth
z_c = np.ceil(patch_size / 2)
z_c_sources = np.zeros(int(z_len / patch_size))
for iz in range(0, int(z_len / patch_size)):
z_c_sources[iz] = (iz * patch_size) + z_c - 1
# Patch's sampling number treshold
TRSH = 0.50
if patch_size == 1 or patch_size == 2:
if vol_slice < 0.010: TRSH = 0
elif vol_slice < 0.035: TRSH = 0.15
elif vol_slice < 0.070 and vol_slice >= 0.035: TRSH = 0.60
elif vol_slice >= 0.070: TRSH = 0.80
elif patch_size == 4 or patch_size == 8:
if vol_slice < 0.035: TRSH = 0
''' Extracting Source Patches '''
print("Extracting source patches.")
print(str(source_patch_len) + " source patches to extract...")
icv_source_flag = np.zeros([source_patch_len])
index_mapping = np.ones([source_patch_len]) * -1
index = 0
index_source= 0
## If patch_size == 1, avoid heavy computation
if patch_size == 1:
area_source_patch = input_mri_data[mri_mask == 1]
area_source_patch = area_source_patch.reshape([area_source_patch.shape[0], 1, 1, 1])
index = source_patch_len
index_source = area_source_patch.shape[0]
icv_source_flag = mri_mask.flatten()
positive_indices = (np.where(input_mri_data.flatten() > 0))[0]
index = 0
for i in positive_indices:
index_mapping[i] = index
index += 1
else:
area_source_patch = []
for isc in range(0, counter_x):
for jsc in range(0, counter_y):
for ksc in range(0, counter_z):
icv_source_flag[index] = mri_mask[int(x_c_sources[isc]), int(y_c_sources[jsc]), int(z_c_sources[ksc])]
if icv_source_flag[index] == 1:
temp = get_volume(x_c_sources[isc], y_c_sources[jsc], z_c_sources[ksc],
patch_size, patch_size, patch_size, input_mri_data)
area_source_patch.append(temp.tolist())
index_mapping[index] = index_source
index_source += 1
index += 1
area_source_patch = np.asarray(area_source_patch)
print("Source patch extraction completed.")
''' Extracting Target Patches '''
print("Extracting target patches.")
## Note: target patches are chosen according to mri_mask and threshold
## if thresholding is enabled, get a thresholded volume of the brain (WMH)
if thrsh_patches != None:
thresholded_brain = get_thresholded_brain(input_mri_data)
patches_rejected = 0
target_patches = []
index_debug = 0
random_array = np.random.randint(10, size=(x_len, y_len, z_len))
index_possible = np.zeros(input_mri_data.shape)
index_possible[(mri_mask != 0) & (random_array > TRSH*10)] = 1
index_possible = np.argwhere(index_possible)
for index_chosen in index_possible:
x, y, z = index_chosen
volume = get_volume(x, y, z, patch_size, patch_size, patch_size, input_mri_data)
if volume.size == patch_size * patch_size * patch_size:
if np.random.randint(low=1, high=10)/10 < (100/(x*y*z)) * num_samples:
pass
if thrsh_patches != None:
thrsh_filter = threshold_filter(thresholded_brain, patch_size, index_chosen, thrsh_patches)
if thrsh_filter == True:
target_patches.append(volume)
index_debug += 1
else:
patches_rejected += 1
else:
target_patches.append(volume)
index_debug += 1
if thrsh_patches != None:
percentage_rejected = round((patches_rejected/index_debug)*100, 1)
print("Number of patches rejected: " + str(patches_rejected) + " (" + str(percentage_rejected) + "%).")
target_patches_np = get_shuffled_patches(target_patches, num_samples)
print('Sampling finished with: ' + str(target_patches_np.shape[0]) + ' samples from: '
+ str(len(target_patches)))
volume = []
''' 3D processing until here'''
''' Reshaping array data for GPU (CUDA) calculation '''
source_patches_all = np.reshape(area_source_patch,(area_source_patch.shape[0],
area_source_patch.shape[1] * area_source_patch.shape[2] * target_patches_np.shape[3]))
target_patches_all = np.reshape(target_patches_np, (target_patches_np.shape[0],
target_patches_np.shape[1] * target_patches_np.shape[2] * target_patches_np.shape[3]))
return source_patches_all, target_patches_all, index_source, index_mapping
def calculate_irregularity_values(source_patches, target_patches, num_mean_samples,
index_source, alpha=0.5):
'''
Calculate irregularity values on GPU (CUDA)
'''
age_values_valid = np.zeros(index_source)
brain_mask = np.ones(index_source)
source_len = index_source
loop_len = 512 # def: 512
loop_num = int(np.ceil(source_len / loop_len))
print('\nLoop Information:')
print('Total number of source patches: ' + str(source_len))
print('Number of voxels processed in one loop: ' + str(loop_len))
print('Number of loop needed: ' + str(loop_num))
print('Check GPU memory: ' + str(cuda.current_context().get_memory_info()))
for il in range(0, loop_num):
''' Debug purposed printing '''
print('.', end='')
if np.remainder(il+1, 32) == 0:
print(' ' + str(il+1) + '/' + str(loop_num)) # Print newline
''' Only process sub-array '''
source_patches_loop = source_patches[il*loop_len:(il*loop_len)+loop_len,:]
''' SUBTRACTION '''
sub_result_gm = cuda.device_array((source_patches_loop.shape[0],
target_patches.shape[0],
target_patches.shape[1]))
TPB = (4,256)
BPGx = int(math.ceil(source_patches_loop.shape[0] / TPB[0]))
BPGy = int(math.ceil(target_patches.shape[0] / TPB[1]))
BPGxy = (BPGx,BPGy)
cu_sub_st[BPGxy,TPB](source_patches_loop, target_patches, sub_result_gm)
''' MAX-MEAN-ABS '''
sub_max_mean_result = cuda.device_array((source_patches_loop.shape[0],
target_patches.shape[0],2))
cu_max_mean_abs[BPGxy,TPB](sub_result_gm, sub_max_mean_result)
sub_result_gm = 0 # Free memory
''' DISTANCE '''
distances_result = cuda.device_array((source_patches_loop.shape[0],
target_patches.shape[0]))
cu_distances[BPGxy,TPB](sub_max_mean_result,
brain_mask[il*loop_len:(il*loop_len)+loop_len],
distances_result, alpha)
sub_max_mean_result = 0 # Free memory
''' SORT '''
TPB = 256
BPG = int(math.ceil(distances_result.shape[0] / TPB))
cu_sort_distance[BPG,TPB](distances_result)
''' MEAN (AGE-VALUE) '''
idx_start = 8 # Starting index of mean calculation (to avoid bad example)
distances_result_for_age = distances_result[:,idx_start:idx_start+num_mean_samples]
distances_result = 0 # Free memory
cu_age_value[BPG,TPB](distances_result_for_age,
age_values_valid[il*loop_len:(il*loop_len)+loop_len])
distances_result_for_age = 0 # Free memory
del source_patches_loop # Free memory
print(' - Finished!\n')
return age_values_valid
def create_output_folders(dirOutput, mri_code):
'''
Create output folders (directories)
'''
dirOutData = dirOutput + '/' + mri_code
dirOutDataCom = dirOutput + '/' + mri_code + '/JPEGs/'
dirOutDataPatch = dirOutput + '/' + mri_code + '/JPEGs/Patch/'
dirOutDataCombined = dirOutput + '/' + mri_code + '/JPEGs/Combined/'
os.makedirs(dirOutData)
os.makedirs(dirOutDataCom)
os.makedirs(dirOutDataPatch)
os.makedirs(dirOutDataCombined)
def keep_relevant_slices(mri_data):
'''
Exclude empty slices
'''
original_index_end = mri_data.shape[2]
index_start = 0
index_end = original_index_end-1
for index in range(0, original_index_end):
if np.count_nonzero(~np.isnan(mri_data[:, :, index])) == 0:
index_start = index
else:
break
for index in range(original_index_end - 1, -1, -1):
if np.count_nonzero(~np.isnan(mri_data[:, :, index])) == 0:
index_end = index
else:
break
print("Only considering relevant slices between indices: [" + str(index_start) + "-" + str(index_end) + "]")
mri_data = mri_data[:, :, index_start:index_end+1]
mri_data = np.nan_to_num(mri_data)
return mri_data, index_start, original_index_end
def reshape_original_dimensions(modified_array, index_start, original_index_end):
'''
Restore the empty slices back.
'''
[x_len, y_len, z_len] = modified_array.shape
index_end = original_index_end - z_len - index_start
top_empty_slices = np.zeros([x_len, y_len, index_start])
bottom_empty_slices = np.zeros([x_len, y_len, index_end])
reshaped_array = np.concatenate((top_empty_slices,modified_array), axis=2)
reshaped_array = np.concatenate((reshaped_array, bottom_empty_slices), axis=2)
return reshaped_array
def kernel_sphere(vol):
'''
Kernel sphere for Gaussian noise (OpenCV library).
'''
if vol == 1 or vol == 2:
return np.array([[1]])
elif vol == 3 or vol == 4:
return np.array([[0,1,0],[1,1,1],[0,1,0]])
elif vol == 5 or vol == 6:
return np.array([[0,0,1,0,0],[0,1,1,1,0],[1,1,1,1,1],[0,1,1,1,0],[0,0,1,0,0]])
elif vol == 7 or vol == 8:
return np.array([[0,0,0,1,0,0,0],[0,1,1,1,1,1,0],[0,1,1,1,1,1,0],[1,1,1,1,1,1,1],
[0,1,1,1,1,1,0],[0,1,1,1,1,1,0],[0,0,0,1,0,0,0]])
elif vol == 9 or vol == 10:
return np.array([[0,0,0,0,1,0,0,0,0],[0,0,1,1,1,1,1,0,0],[0,1,1,1,1,1,1,1,0],[0,1,1,1,1,1,1,1,0],
[1,1,1,1,1,1,1,1,1],[0,1,1,1,1,1,1,1,0],[0,1,1,1,1,1,1,1,0],[0,0,1,1,1,1,1,0,0],
[0,0,0,0,1,0,0,0,0]])
elif vol == 11 or vol > 11:
return np.array([[0,0,0,0,0,1,0,0,0,0,0],[0,0,1,1,1,1,1,1,1,0,0],[0,1,1,1,1,1,1,1,1,1,0],
[0,1,1,1,1,1,1,1,1,1,0],[0,1,1,1,1,1,1,1,1,1,0],[1,1,1,1,1,1,1,1,1,1,1],
[0,1,1,1,1,1,1,1,1,1,0],[0,1,1,1,1,1,1,1,1,1,0],[0,1,1,1,1,1,1,1,1,1,0],
[0,0,1,1,1,1,1,1,1,0,0],[0,0,0,0,0,1,0,0,0,0,0]])
def get_area(x_c, y_c, x_dist, y_dist, img):
'''
Get MRI's intensities (2D).
'''
[x_len, y_len] = img.shape
even_x = np.mod(x_dist, 2) - 2
even_y = np.mod(y_dist, 2) - 2
x_top = x_c - np.floor(x_dist / 2) - (even_x + 1)
x_low = x_c + np.floor(x_dist / 2)
y_left = y_c - np.floor(y_dist / 2) - (even_y + 1)
y_rght = y_c + np.floor(y_dist / 2)
if x_top < 0: x_top = 0
if x_low >= x_len: x_low = x_len
if y_left < 0: y_left = 0
if y_rght >= y_len: y_rght = y_len
area = img[int(x_top):int(x_low+1),int(y_left):int(y_rght+1)]
return area
def get_volume(x_c, y_c, z_c, x_dist, y_dist, z_dist, brain):
'''
Get MRI's intensities (3D).
'''
[x_len, y_len, z_len] = brain.shape
even_x = np.mod(x_dist, 2) - 2
even_y = np.mod(y_dist, 2) - 2
even_z = np.mod(z_dist, 2) - 2
x_top = x_c - np.floor(x_dist / 2) - (even_x + 1)
x_low = x_c + np.floor(x_dist / 2)
y_left = y_c - np.floor(y_dist / 2) - (even_y + 1)
y_rght = y_c + np.floor(y_dist / 2)
z_front = z_c - np.floor(z_dist / 2) - (even_z + 1)
z_back = z_c + np.floor(z_dist / 2)
if x_top < 0: x_top = 0
if x_low >= x_len: x_low = x_len
if y_left < 0: y_left = 0
if y_rght >= y_len: y_rght = y_len
if z_front < 0: z_front = 0
if z_back >= z_len: z_back = z_len
volume = brain[int(x_top):int(x_low+1),int(y_left):int(y_rght+1),int(z_front):int(z_back+1)]
return volume
def get_thresholded_brain(mri_data):
'''
Early estimate the WMH using confidence interval (CI).
'''
mri_data = mri_data/np.nanmax(np.nanmax(np.nanmax(mri_data)))
scan_mean = np.sum(mri_data[mri_data > 0]) / np.sum(mri_data > 0)
scan_std = np.std(mri_data[mri_data > 0])
mri_std = np.true_divide((mri_data-scan_mean), scan_std)
WMH = np.zeros(mri_data.shape)
iWMH = np.zeros(mri_data.shape)
WMH[np.nan_to_num(mri_data) >= (scan_mean + (1.282 * scan_std))] = 1 # Less intense regions
iWMH[np.nan_to_num(mri_data) >= (scan_mean + (1.69 * scan_std))] = 1 # Very intense regions
for zz in range(WMH.shape[2]):
layer_iWMH = iWMH[:, :, zz]
kernel = np.ones((2,2),np.uint8)
layer_iWMH = cv2.erode(layer_iWMH, kernel, iterations = 1)
iWMH[:, :, zz] = layer_iWMH
iWMH[iWMH > 0] = 1
return iWMH
def gaussian_3d(thresholded_brain):
'''
Calculate 3D Gaussian blur.
'''
## Based on https://stackoverflow.com/questions/45723088/
## how-to-blur-3d-array-of-points-while-maintaining-their-original-values-python
sigma = 1.0
x = np.arange(-1,2,1)
y = np.arange(-1,2,1)
z = np.arange(-1,2,1)
xx, yy, zz = np.meshgrid(x,y,z)
kernel = np.exp(-(xx**2 + yy**2 + zz**2)/(2*sigma**2))
return signal.convolve(thresholded_brain, kernel, mode="same")
def threshold_filter(thresholded_brain, patch_size, index_chosen, threshold):
'''
Reject/accept target patch which has a certain number of early estimated WMH.
'''
threshold = (patch_size*patch_size*patch_size) * threshold
x, y, z = index_chosen
WMH_volume = get_volume(x, y, z, patch_size, patch_size, patch_size, thresholded_brain)
if np.count_nonzero(WMH_volume) > threshold:
return False
return True
def get_shuffled_patches(target_patches_list, num_samples):
'''
Shuffle the target patches.
'''
shuffled_list = [target_patches_list[index] for index in random.sample(range(len(target_patches_list)), num_samples)]
shuffled_array = np.asarray(shuffled_list)
return shuffled_array
def get_slice_irregularity_map(patch_size, mat_contents, mask_slice):
'''
Read irregularity map of each file from intermediary .mat file.
'''
slice_age_map = mat_contents['slice_irregularity_map']
slice_age_map_res = cv2.resize(slice_age_map, None, fx=patch_size,
fy=patch_size, interpolation=cv2.INTER_CUBIC)
slice_age_map_res = skifilters.gaussian(slice_age_map_res,sigma=0.5,truncate=2.0)
slice_age_map_res = np.multiply(mask_slice, slice_age_map_res)
return slice_age_map_res