def setAngleFilename_fromLineEdit(self):
filename = self.ui.lineEdit_angleFile.text()
if os.path.isfile(toString(filename)):
self.calculationParameters.angleFilename = filename
self.calculationParameters.angleFileProvided = True
self.ui.lineEdit_angleFile.setText(toQString(filename))
self.disableAngleWidgets()
def loadModel(self, filename):
self.calculationParameters.oversamplingRatio, ok = QtWidgets.QInputDialog.getInt(
self,
"Select Oversampling Ratio",
"Oversampling Ratio = ",
value=3,
min=1,
max=10,
step=1)
from threading import Thread
t = Thread(target=lambda: print("Loading Model..."))
t.start()
self.ui.btn_go.setEnabled(True)
self.calculationParameters.model = genfire.fileio.readVolume(
toString(filename))
self.calculationParameters.dims = np.shape(
self.calculationParameters.model)
self.calculationParameters.paddedDim = self.calculationParameters.dims[
0] * self.calculationParameters.oversamplingRatio
padding = int((self.calculationParameters.paddedDim -
self.calculationParameters.dims[0]) / 2)
self.calculationParameters.model = np.pad(
self.calculationParameters.model,
((padding, padding), (padding, padding), (padding, padding)),
'constant')
self.calculationParameters.model = fftn_fftshift(
self.calculationParameters.model)
self.calculationParameters.ncOut = int(
np.shape(self.calculationParameters.model)[0] // 2)
self.calculationParameters.interpolator = genfire.utility.getProjectionInterpolator(
self.calculationParameters.model)
t.join()
def launchVolumeSlicer(self):
import genfire.fileio
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select Volume",
filter="Volume files (*.mat *.mrc *.npy);;All Files (*)")
if filename:
filename = toString(filename)
volume = genfire.fileio.readVolume(filename)
self.VolumeSlicer = VolumeSlicer.VolumeSlicer(volume)
self.VolumeSlicer.show()
def selectModelFile(self):
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select File Containing Model",
filter=
"Volume files (*.mrc *.mat *.npy);;MATLAB files (*.mat);;TIFF images (*.tif *.tiff);;MRC (*.mrc);;numpy (*.npy);;All Files (*)"
)
print(filename)
if os.path.isfile(toString(filename)):
self.ui.btn_go.setEnabled(True)
self.setModelFilename(filename)
def updateFilenames(self):
import os
base, file = os.path.split(
toString(self.GENFIRE_ProjectionCalculator.calculationParameters.
outputFilename))
self.ui.lineEdit_angle.setText(
toQString(
str(self.GENFIRE_ProjectionCalculator.calculationParameters.
outputAngleFilename)))
self.ui.lineEdit_angle.textChanged.emit(self.ui.lineEdit_angle.text())
self.ui.lineEdit_pj.setText(
toQString(
str(self.GENFIRE_ProjectionCalculator.calculationParameters.
outputFilename)))
self.ui.lineEdit_pj.textChanged.emit(self.ui.lineEdit_pj.text())
self.ui.lineEdit_results.setText(toQString(str(base + "/results.mrc")))
self.ui.lineEdit_results.textChanged.emit(
self.ui.lineEdit_results.text())
def displayResults(self):
outputfilename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select Reconstruction",
filter=
"Volume files (*.mrc *.mat *.npy) ;; MATLAB files (*.mat);;text files (*.txt *.tiff);;MRC (*.mrc);;All Files (*)"
)
outputfilename = toString(outputfilename)
if outputfilename:
import numpy as np
import os
import genfire.fileio
import matplotlib.pyplot as plt
plt.close('all')
initialObject = genfire.fileio.readVolume(outputfilename)
dims = np.shape(initialObject)
n_half_x = int(dims[0] / 2) #this assumes even-sized arrays
n_half_y = int(dims[1] / 2)
n_half_z = int(dims[2] / 2)
reconstructionDisplayWindowSize = dims[0] # array should be cubic
half_window_x = reconstructionDisplayWindowSize // 2
half_window_y = reconstructionDisplayWindowSize // 2
half_window_z = reconstructionDisplayWindowSize // 2
plt.figure()
plt.subplot(233)
plt.imshow(
np.squeeze(initialObject[n_half_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z]))
plt.title("central YZ slice")
plt.subplot(232)
plt.imshow(
np.squeeze(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x, n_half_y,
n_half_z - half_window_z:n_half_z +
half_window_z]))
plt.title("central XZ slice")
plt.subplot(231)
plt.title("central XY slice")
plt.imshow(
np.squeeze(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y, n_half_z]))
plt.subplot(236)
plt.title("YZ projection")
plt.imshow(
np.squeeze(
np.sum(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z],
axis=0)))
plt.subplot(235)
plt.title("XZ projection")
plt.imshow(
np.squeeze(
np.sum(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z],
axis=1)))
plt.subplot(234)
plt.title("XY projection")
plt.imshow(
np.squeeze(
np.sum(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z],
axis=2)))
plt.get_current_fig_manager().window.setGeometry(25, 25, 600, 1200)
# now load error curves if they exist
output_base, output_ext = os.path.splitext(outputfilename)
errK_filename = output_base + '_errK.txt'
if os.path.isfile(errK_filename):
errK = np.loadtxt(errK_filename)
numIterations = np.shape(errK)[0]
plt.figure()
plt.plot(range(0, numIterations), errK)
mngr = plt.get_current_fig_manager()
mngr.window.setGeometry(700, 25, 550, 250)
plt.title("Reciprocal Error vs Iteration Number")
plt.xlabel("Iteration Num")
plt.ylabel("Reciprocal Error")
# plt.setp(plt.gcf(),)
Rfree_total_filename = output_base + '_Rfree_total.txt'
Rfree_bybin_filename = output_base + '_Rfree_bybin.txt'
if os.path.isfile(Rfree_total_filename):
Rfree_total = np.loadtxt(Rfree_total_filename)
numIterations = np.shape(Rfree_total)[0]
plt.figure()
plt.title("R-free vs Iteration Number")
mngr = plt.get_current_fig_manager()
mngr.window.setGeometry(700, 350, 550, 250)
plt.plot(range(0, numIterations), Rfree_total)
plt.title("Mean R-free Value vs Iteration Number")
plt.xlabel("Iteration Num")
plt.ylabel('Mean R-free')
if os.path.isfile(Rfree_bybin_filename):
Rfree_bybin = np.loadtxt(Rfree_bybin_filename)
plt.figure()
mngr = plt.get_current_fig_manager()
mngr.window.setGeometry(700, 650, 550, 250)
X = np.linspace(0, 1, np.shape(Rfree_bybin)[0])
plt.plot(X, Rfree_bybin[:, -1])
plt.title("Final Rfree Value vs Spatial Frequency")
plt.xlabel("Spatial Frequency (% of Nyquist)")
plt.ylabel('Rfree')
plt.draw()
plt.pause(1e-30) # slight pause forces redraw
def setModelFilename_fromLineEdit(self):
filename = self.ui.lineEdit_modelFile.text()
if os.path.isfile(
toString(filename)
) and filename != self.calculationParameters.modelFilename:
self.setModelFilename(toString(filename))
def calculateProjections(self):
if self.calculateProjections_Dialog.status:
self.calculationParameters.modelFilename = toString(
self.calculationParameters.modelFilename)
if not self.calculationParameters.modelLoadedFlag:
self.calculationParameters.model = genfire.fileio.readVolume(
self.calculationParameters.modelFilename)
self.calculationParameters.oversamplingRatio = self.calculationParameters.oversamplingRatio
self.calculationParameters.dims = np.shape(
self.calculationParameters.model)
paddedDim = self.calculationParameters.dims[
0] * self.calculationParameters.oversamplingRatio
padding = int(
(paddedDim - self.calculationParameters.dims[0]) / 2)
self.calculationParameters.model = np.pad(
self.calculationParameters.model,
((padding, padding), (padding, padding),
(padding, padding)), 'constant')
self.calculationParameters.model = fftn_fftshift(
self.calculationParameters.model)
self.calculationParameters.interpolator = genfire.utility.getProjectionInterpolator(
self.calculationParameters.model)
self.calculationParameters.ncOut = np.shape(
self.calculationParameters.model)[0] // 2
if self.calculationParameters.angleFileProvided:
self.calculationParameters.angleFilename = toString(
self.calculationParameters.angleFilename)
self.calculationParameters.outputFilename = toString(
self.calculationParameters.outputFilename)
angles = np.loadtxt(
toString(self.calculationParameters.angleFilename))
phi = angles[:, 0]
theta = angles[:, 1]
psi = angles[:, 2]
filename = self.calculationParameters.outputFilename + '.npy'
projections = np.zeros(
(self.calculationParameters.dims[0],
self.calculationParameters.dims[1], np.size(phi)),
dtype=float)
if self.calculationParameters.interpolator is None:
self.calculationParameters.interpolator = genfire.utility.getProjectionInterpolator(
self.calculationParameters.model)
for projNum in range(0, np.size(phi)):
pj = genfire.utility.calculateProjection_interp_fromInterpolator(
self.calculationParameters.interpolator, phi[projNum],
theta[projNum], psi[projNum],
np.shape(self.calculationParameters.model))
projections[:, :, projNum] = pj[
self.calculationParameters.ncOut -
int(self.calculationParameters.dims[0] /
2):self.calculationParameters.ncOut +
int(self.calculationParameters.dims[0] / 2),
self.calculationParameters.ncOut -
int(self.calculationParameters.dims[1] /
2):self.calculationParameters.ncOut +
int(self.calculationParameters.dims[1] / 2)]
genfire.fileio.writeVolume(filename, projections)
else:
if self.calculationParameters.interpolator is None:
self.calculationParameters.interpolator = genfire.utility.getProjectionInterpolator(
self.calculationParameters.model)
phi = self.calculationParameters.phi
psi = self.calculationParameters.psi
theta = np.arange(self.calculationParameters.thetaStart, \
self.calculationParameters.thetaStop + 1e-10, \
self.calculationParameters.thetaStep)
projections = np.zeros(
(self.calculationParameters.dims[0],
self.calculationParameters.dims[1], np.size(theta)),
dtype=float)
for i, current_theta in enumerate(theta):
pj = genfire.utility.calculateProjection_interp_fromInterpolator(
self.calculationParameters.interpolator, phi,
current_theta, psi,
np.shape(self.calculationParameters.model))
projections[:, :, i] = pj[
self.calculationParameters.ncOut -
int(self.calculationParameters.dims[0] /
2):self.calculationParameters.ncOut +
int(self.calculationParameters.dims[0] / 2),
self.calculationParameters.ncOut -
int(self.calculationParameters.dims[1] /
2):self.calculationParameters.ncOut +
int(self.calculationParameters.dims[1] / 2)]
filename = self.calculationParameters.outputFilename
filename = toString(filename)
# projections[ projections<0 ] = 0
genfire.fileio.writeVolume(filename, projections)
if self.calculationParameters.writeAnglesFlag:
output_filename_base, ext = os.path.splitext(
toString(self.calculationParameters.outputFilename))
output_angle_filename = output_filename_base + "_euler_angles.txt"
if os.path.isfile(output_angle_filename):
print(
"WARNING! Filename {} already exists and will be overwritten."
.format(output_angle_filename))
self.calculationParameters.outputAngleFilename = output_angle_filename
num_projections = np.size(theta)
phi = np.repeat(phi, num_projections)
psi = np.repeat(psi, num_projections)
with open(output_angle_filename, 'w') as fid:
for euler in zip(phi, theta, psi):
string = str(euler[0]) + ' ' + str(
euler[1]) + ' ' + str(euler[2]) + '\n'
fid.write(string)
print("Successfully calculated {}.".format(
output_angle_filename))
print("Successfully calculated {}.".format(filename))
