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Commit 434e9c23 authored by Jonathan Juhl's avatar Jonathan Juhl
Browse files

added relative path and removed voltage bug

parent eb6e00c2
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execute_sortem.py
View file @ 434e9c23
import numpy as np
import os
from super_clas_sortem import super_class
from os.path import join,getsize,isdir,isfile,dirname,basename
from os import listdir,rename
......@@ -10,6 +11,8 @@ from os import listdir,mkdir
import glob
from os.path import isabs
from fac_sortem import DynAE
class control_flow:
......@@ -49,9 +52,11 @@ class control_flow:
heads = []
head = []
counter = 0
for i in header:
if 'loop_' == i:
counter+=1
head = []
heads.append(head)
else:
......@@ -59,16 +64,20 @@ class control_flow:
take_this = []
for i in heads:
if '_rlnVoltage' in i:
take_that = i
if '_rlnImageName' in i:
take_this = i
header = take_this
name = header.index('_rlnImageName')
voltage = header.index('_rlnVoltage')
voltage = take_that.index('_rlnVoltage')
defocusU = header.index('_rlnDefocusU')
defocusV = header.index('_rlnDefocusV')
defocusAngle = header.index('_rlnDefocusAngle')
abberation = header.index('_rlnSphericalAberration')
amp_contrast = header.index('_rlnAmplitudeContrast')
abberation = take_that.index('_rlnSphericalAberration')
amp_contrast = take_that.index('_rlnAmplitudeContrast')
phase_shift = header.index('_rlnPhaseShift')
ctf_params = []
......@@ -82,6 +91,13 @@ class control_flow:
print("the --log true cannot be run as _rlnClassNumber i missing ")
for row in reader:
if len(take_that) == len(row.split()) and counter ==2:
abberation_d = float(row.split()[abberation])
amp_contrast_d = float(row.split()[amp_contrast])
V = float(row.split()[voltage])
electron_volts = (1.23*10**3)/np.sqrt(V*(V*10**(-7)*1.96+1))
counter = 0
if len(header)== len(row.split()):
......@@ -95,16 +111,18 @@ class control_flow:
names.append(join(c,current_name))
if self.verbose:
labels_list.append(int(row.split()[class_num]))
V = float(row.split()[voltage])
electron_volts = (1.23*10**3)/np.sqrt(V*(V*10**(-7)*1.96+1))
abberation_d = float(row.split()[abberation])
amp_contrast_d = float(row.split()[amp_contrast])
if counter == 1:
V = float(row.split()[voltage])
electron_volts = (1.23*10**3)/np.sqrt(V*(V*10**(-7)*1.96+1))
abberation_d = float(row.split()[abberation])
amp_contrast_d = float(row.split()[amp_contrast])
counter = 0
ctf_params.append([float(row.split()[phase_shift]),float(row.split()[defocusU]),float(row.split()[defocusV]),float(row.split()[defocusAngle])])
current_id = row.split()[name].split('@')[0]
np.save(join(self.particle_stack_dir,'depth.npy'),f)
np.save(join(self.particle_stack_dir,'names.npy'),names)
np.save(join(self.particle_stack_dir,'electron_volts.npy'),electron_volts)
......@@ -115,18 +133,20 @@ class control_flow:
return f,np.unique(names)
dir_path = os.path.dirname(os.path.realpath(__file__))
if not isinstance(self.star, list) and isdir(star):
star_files = glob.glob(self.star)
if star_files == []:
print("no star files in directory. You must point to atleast one star file to run Sortinator.")
exit()
star_files = [join(star,i) for i in star_files]
star_files = [join(dir_path,join(star,i)) for i in star_files]
else:
star_files = self.star
star_files = [join(dir_path,i) for i in self.star]
if not isfile(join(self.particle_stack_dir,'depth.npy')):
depth,mrc_paths = get_star_file_parameters(star_files)
......
fac_sortem.py
View file @ 434e9c23
......@@ -132,7 +132,7 @@ class DynAE(super_class):
# tmp = tf.expand_dims(tf.sqrt(tf.abs(ctf_applied_image)),axis=-1)
# generated_image = tf.expand_dims(fake_model,axis=-1) #+ sigma*tmp
#print(generated_image);exit()
h5_sig_f, h5, predict_z, d_h1_f, d_h2_f, d_h3_f, d_h4_f,predict_angels = self.D(fake_model)
h5_sig_f, h5, predict_z, d_h1_f, d_h2_f, d_h3_f, d_h4_f,predict_angels = self.D(fake_projections)
h5_sig_r, h5, _, d_h1_r, d_h2_r, d_h3_r, d_h4_r,predict_angels_real = self.D(x_real)
loss_tot = loss_disc(d_h1_r,d_h1_f,d_h2_r,d_h2_f,d_h3_r,d_h3_f,d_h4_r,d_h4_f,h5_sig_r,h5_sig_f,predict_z,z,predict_angels,angels)
......
models.py
View file @ 434e9c23
......@@ -15,15 +15,13 @@ def AdaIn_3D(inputs,s1,b1):
d= tf.shape(inputs)[3]
c= tf.shape(inputs)[4]
tmp = Flatten()(inputs)
inputs = Flatten()(inputs)
mean = tf.reduce_mean(tmp,axis=1)
std = tf.math.reduce_std(tmp,axis=1)
out = s1*((inputs - mean)/std) + b1
mean = tf.reduce_mean(inputs,axis=1,keepdims=True)
std = tf.math.reduce_std(inputs,axis=1,keepdims=True)
inputs = tf.reshape(((inputs - mean)/std),[b,w,h,d,c])
out = tf.transpose(s1*tf.transpose(inputs,perm=[1,2,3,0,4]) + b1,perm=[3,0,1,2,4])
out = tf.reshape(out,[b,w,h,d,c])
return out
def AdaIn_2D(inputs,s1,b1):
......@@ -33,12 +31,13 @@ def AdaIn_2D(inputs,s1,b1):
c= tf.shape(inputs)[3]
inputs = Flatten()(inputs)
mean = tf.reduce_mean(inputs,axis=1)
std = tf.math.reduce_std(inputs,axis=1)
out = s1*((inputs - mean)/std) + b1
out = tf.reshape(out,[b,w,h,c])
mean = tf.reduce_mean(inputs,axis=1,keepdims=True)
std = tf.math.reduce_std(inputs,axis=1,keepdims=True)
inputs = tf.reshape(((inputs - mean)/std),[b,w,h,c])
out = tf.transpose(s1*tf.transpose(inputs,perm=[1,2,0,3]) + b1,perm=[2,0,1,3])
return out
class Double_Dense(Model):
def __init__(self,channels):
......@@ -140,10 +139,10 @@ class Generator_AdaIN_Noise(Model):
class Generator_AdaIN_res128(Model):
def __init__(self,gf_dim=32):
self.gf_dim = gf_dim
super(Generator_AdaIN_res128,self).__init__()
self.trans_3d = transform_3D()
self.gf_dim = gf_dim
self.h0= Conv3DTranspose( self.gf_dim * 8,3,strides=2)
self.zmap_0 = Double_Dense( self.gf_dim * 8)
......@@ -202,29 +201,30 @@ class Generator_AdaIN_res128(Model):
def call(self,x,psi,phi,rho):
a,b = self.zmap_0(x)
x = self.h0(x)
def call(self,z,psi,phi,rho):
a,b = self.zmap_0(z)
x = self.h0(z)
x = self.h0_aI(x,a,b)
x = self.h0_a(x)
x = self.h1(x)
a,b = self.z_map_1(x)
print(x,a,b),exit()
a,b = self.z_map_1(z)
x = self.h1_aI(x,a,b)
a,b = self.z_map_2(x)
a,b = self.z_map_2(z)
x = self.h2_aI(x,a,b)
x = self.h2(x)
x = transform_3D(x,psi,phi,rho)
x = self.trans_3d(x,psi,phi,rho)
x = self.h2_proj1(x)
x = self.h2_proj1_a(x)
x = self.h2_proj2(x)
x = self.h2_proj2_a(x)
b,w,h,d,c = tf.shape(x)
x = tf.reshape(x, [b,w,h,d*c])
s = tf.shape(x)
x = tf.reshape(x, [s[0],s[1],s[2],s[3]*s[4]])
x = self.h4(x)
x = self.h4_a(x)
......@@ -244,6 +244,7 @@ class Generator_AdaIN_res128(Model):
x = self.h8_a(x)
x = self.h9(x)
return x
class Discriminator_AdaIN_res128(Model):
......
utils_sortem.py
View file @ 434e9c23
......@@ -3,7 +3,6 @@ import tensorflow as tf
import numpy as np
from os.path import join
import tensorflow_addons as tfa
import mrcfile
import matplotlib.pyplot as plt
import math
from tensorflow.keras.layers import Dense,LeakyReLU
......@@ -58,23 +57,11 @@ class transform_3D(tf.keras.layers.Layer):
beta =2*3.1415*tf.cast(beta,tf.float32)
gamma = 2*3.1415*tf.cast(gamma,tf.float32)
voxels = tf.transpose(voxels,perm=[1,2,3,0,4])
dimensions = tf.shape(voxels)[0]
x = tf.cast(tf.range(-tf.cast(tf.floor(tf.cast(dimensions,tf.float32)/2.0),tf.int32),tf.cast(tf.cast(dimensions,tf.float32)-tf.floor(tf.cast(dimensions,tf.float32)/2.0),tf.int32)),tf.float32)
X,Y,Z = tf.meshgrid(x,x,x)
tmp = tf.reshape(voxels,[-1])
X = tf.reshape(X,[-1]); Y = tf.reshape(Y,[-1]);Z = tf.reshape(Z,[-1])
X_mass = tf.round(tf.reduce_mean(X*tmp))
Y_mass = tf.round(tf.reduce_mean(Y*tmp))
Z_mass = tf.round(tf.reduce_mean(Z*tmp))
coordinates = tf.stack([X,Y,Z],axis=0)
kernel = tf.cast(coordinates,tf.float32)
channels = tf.shape(voxels)[-1]
batchdim = tf.shape(voxels)[-2]
rotation_matrix_x =tf.stack([tf.constant(1.0),tf.constant(0.0),tf.constant(0.0),
tf.constant(0.0),tf.cos(alpha), -tf.sin(alpha),
......@@ -93,26 +80,26 @@ class transform_3D(tf.keras.layers.Layer):
rotation_matrix_y = tf.reshape(rotation_matrix_y, (3,3))
rotation_matrix_z = tf.reshape(rotation_matrix_z, (3,3))
s = tf.matmul(rotation_matrix_x,tf.matmul(rotation_matrix_y,rotation_matrix_z))
r = tf.matmul(tf.matmul(rotation_matrix_x,tf.matmul(rotation_matrix_y,rotation_matrix_z)) ,kernel)
r = tf.matmul(tf.matmul(rotation_matrix_x,tf.matmul(rotation_matrix_y,rotation_matrix_z)) ,self.kernel)
x,y,z = tf.split(r,3,axis=0)
X = tf.reshape(x,[-1])
Y = tf.reshape(y,[-1])
Z = tf.reshape(z,[-1])
X_lower = tf.math.floor(X)-X_mass # tf.clip_by_value(tf.math.floor(X),0,self.dimensions)
X_upper = tf.math.ceil(X)-X_mass # tf.clip_by_value(tf.math.ceil(X),0,self.dimensions)
X_lower = tf.math.floor(X) # tf.clip_by_value(tf.math.floor(X),0,self.dimensions)
X_upper = tf.math.ceil(X) # tf.clip_by_value(tf.math.ceil(X),0,self.dimensions)
Y_lower = tf.math.floor(Y)-Y_mass # tf.clip_by_value(tf.math.floor(Y),0,self.dimensions)
Y_upper = tf.math.ceil(Y)-Y_mass # tf.clip_by_value(tf.math.ceil(Y),0,self.dimensions)
Y_lower = tf.math.floor(Y) # tf.clip_by_value(tf.math.floor(Y),0,self.dimensions)
Y_upper = tf.math.ceil(Y) # tf.clip_by_value(tf.math.ceil(Y),0,self.dimensions)
Z_lower = tf.math.floor(Z)-Z_mass # tf.clip_by_value(tf.math.floor(Z),0,self.dimensions)
Z_upper = tf.math.ceil(Z)-Z_mass #tf.clip_by_value(tf.math.ceil(Z),0,self.dimensions)
Z_lower = tf.math.floor(Z) # tf.clip_by_value(tf.math.floor(Z),0,self.dimensions)
Z_upper = tf.math.ceil(Z) #tf.clip_by_value(tf.math.ceil(Z),0,self.dimensions)
x_d = (X-X_lower+0.001)/(X_upper-X_lower+0.001)
y_d = (Y-Y_lower+0.001)/(Y_upper-Y_lower+0.001)
z_d = (Z-Z_lower+0.001)/(Z_upper-Z_lower+0.001)
coord_000 = tf.stack([X_lower,Y_lower,Z_lower],axis=1)+tf.cast(tf.floor(dimensions/2),tf.float32)
coord_001 = tf.stack([X_lower,Y_lower,Z_upper],axis=1)+tf.cast(tf.floor(dimensions/2),tf.float32)
coord_011 = tf.stack([X_lower,Y_upper,Z_upper],axis=1)+tf.cast(tf.floor(dimensions/2),tf.float32)
......@@ -129,7 +116,11 @@ class transform_3D(tf.keras.layers.Layer):
c100 = tf.gather_nd(voxels,tf.cast(coord_100,tf.int32))
c010 = tf.gather_nd(voxels,tf.cast(coord_010,tf.int32))
c110 = tf.gather_nd(voxels,tf.cast(coord_110,tf.int32))
x_d = tf.expand_dims(tf.expand_dims(x_d,axis=1),axis=1)
y_d = tf.expand_dims(tf.expand_dims(y_d,axis=1),axis=1)
z_d = tf.expand_dims(tf.expand_dims(z_d,axis=1),axis=1)
c00 = c000*(1-x_d) + c100*x_d
c01 = c001*(1-x_d) + c101*x_d
c10 = c010*(1-x_d) + c110*x_d
......@@ -137,13 +128,18 @@ class transform_3D(tf.keras.layers.Layer):
c0 = c00*(1-y_d) + c10*y_d
c1 = c01*(1-y_d) + c11*y_d
c = c0*(1-z_d)+c1*z_d
return tf.reduce_sum(tf.reshape(c,[dimensions,dimensions,dimensions]),axis=0)
c = tf.transpose(c,perm=[1,0,2])
out = tf.reshape(c,[batchdim,dimensions,dimensions,dimensions,channels])
return out
def call(self,voxels,alpha,beta,gamma):
image =tf.expand_dims(tf.map_fn(lambda x: self.rotation_map(tf.squeeze(voxels),x[0],x[1],x[2]),[alpha,beta,gamma],dtype=tf.float32),axis=-1)
s = tf.shape(image)
image = tf.reshape(image,[s[0]*s[1],s[2],s[3],s[4],s[5]])
return image
......@@ -312,11 +308,13 @@ def apply_ctf(image,ctf_params,gamma,spherical_abberation,w_2):
return tf.cast(image,tf.float32)
def z_maker(model,num_linear_params):
k = np.random.random(num_linear_params)
#k = k/np.sum(k)
z = np.dot(model,k)
s = np.cbrt(z.shape[0]).astype(np.int32)
z = np.reshape(z,[1,s,s,s,1])
z = np.concatenate([z]*10,axis=0)
return z,k
......
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