TIGRE/Python/tests/algorithm_test.py at master · Pawelip/TIGRE · GitHub

History

142 lines (124 loc) · 5.2 KB

Raw

100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

import os

import sys

import time

import traceback

import numpy as np

import tigre

from matplotlib import pyplot as plt

from tigre.demos.Test_data.data_loader import load_head_phantom

from tigre.utilities.Measure_Quality import Measure_Quality

class AlgorithmTest(object):

def __init__(self, configuration, algorithm, **kwargs):

"""

:param configuration: (str)

which predefined Configuration to use

:param algorithm: (str)

which algorithm to test

"""

self.dirname = os.path.dirname(__file__)

self.targetdir = str(

np.load(os.path.join(self.dirname, "targetdir.npy"), allow_pickle=True)

)

configdict = np.load(os.path.join(self.dirname, configuration), allow_pickle=True).item()

for key in configdict:

"""contains: [nproj,geo,angles,niter,kwargs]"""

setattr(self, key, configdict[key])

self.algorithm = algorithm

self.testpassed = False

self.algorithm_finished = False

self.rmse = 1.0

self.confignumber = os.path.splitext(configuration)[0]

self.output = None

self.timestarted = time.asctime()

self.timeended = time.asctime()

def test(self):

head = load_head_phantom(self.geo.nVoxel)

proj = tigre.Ax(head, self.geo, self.angles)

if self.algorithm in ["FDK", "fbp"]:

self.output = getattr(tigre.algorithms, self.algorithm)(proj, self.geo, self.angles)

self.rmse = Measure_Quality(self.output, head, ["nRMSE"])

self.algorithm_finished = True

return

self.timestarted = time.asctime()

self.output = getattr(tigre.algorithms, self.algorithm)(

proj, self.geo, self.angles, self.niter, **self.kwargs

)

self.timeended = time.asctime()

self.algorithm_finished = True

self.rmse = Measure_Quality(self.output, head, ["nRMSE"])

def unit_test_call(self):

self.test()

self.compound_results()

return self.testpassed

def compound_results(self, verbose=True):

if self.algorithm_finished and self.rmse < 0.2:

self.testpassed = True

elif self.algorithm == "sirt" and self.algorithm_finished and self.rmse < 0.3:

self.testpassed = True

else:

print("===================================================")

print("TEST FAILED")

print("Algorithm: " + self.algorithm)

print("Algorithm ran: " + str(self.algorithm_finished))

print("configuration number: " + str(self.confignumber))

print("RMSE:" + str(self.rmse))

print("===================================================")

def save_output(self):

resultfilename = self.confignumber + ".npy"

try:

resultsdata = np.load(

os.path.join(self.targetdir, resultfilename), allow_pickle=True

).item()

except Exception:

resultsdata = {}

resultsdata.update({self.algorithm: self.testpassed})

np.save(os.path.join(self.targetdir, resultfilename), resultsdata)

if not self.testpassed:

self.write_to_log()

def save_fig(self):

res = self.output

geo = self.geo

plt.figure()

plt.subplot(3, 1, 1)

plt.imshow(res[geo.nVoxel[0] / 2])

plt.title("results for " + self.algorithm)

plt.ylabel("dim 0")

plt.subplot(3, 1, 2)

plt.imshow(res[:, geo.nVoxel[1] / 2])

plt.ylabel("dim 1")

plt.subplot(3, 1, 3)

plt.imshow(res[:, :, geo.nVoxel[2] / 2])

plt.ylabel("dim 2")

plt.savefig(os.path.join(self.targetdir, self.algorithm + self.confignumber))

def write_to_log(self):

configlogfile = self.confignumber + ".log"

logflist = []

if configlogfile not in os.listdir(self.targetdir):

logflist.append("GEOMETRY used for instance of testandlog: \n")

for item in self.geo.__dict__:

logflist.append(item + ": " + str(getattr(self.geo, item)) + "\n")

logflist.append(

"nproj: " + str(self.angles.shape[0]) + " niter: " + str(self.niter) + "\n"

)

logflist.append("------------------------------------------------\n")

else:

logflist.extend(open(os.path.join(self.targetdir, configlogfile), "r").readlines())

logflist.append(str(self.algorithm).upper() + " " + str(self.timestarted) + "\n")

logflist.append("RMSE: " + str(self.rmse) + "\n")

logflist.append("Algorithm ran: " + str(self.algorithm_finished) + "\n")

if self.algorithm_finished:

logflist.append("ENDED: " + str(self.timeended) + "\n")

logflist.append("------------------------------------------------\n")

with open(os.path.join(self.targetdir, configlogfile), "w") as logf:

logf.write("".join(logflist))

if __name__ == "__main__":

configuration = sys.argv[1]

algorithm = sys.argv[2]

test = AlgorithmTest(configuration, algorithm)

try:

test.test()

except Exception:

formatedlines = traceback.format_exc()

print(formatedlines)

test.compound_results()

test.save_output()

TIGRE/Python/tests/algorithm_test.py at master · Pawelip/TIGRE · GitHub

Expand file tree

Breadcrumbs

algorithm_test.py

Latest commit

History

Breadcrumbs

algorithm_test.py

File metadata and controls