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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Fast Azimuthal Integration
# https://github.com/pyFAI/pyFAI
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
#
"test suite for peak picking class"
__author__ = "Jérôme Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "20140703"
import unittest
import os
import numpy
import logging, time
import sys
import fabio
from utilstest import UtilsTest, Rwp, getLogger
logger = getLogger(__file__)
pyFAI = sys.modules["pyFAI"]
NO_PEAK_PICKER = False
try:
import pyFAI.peak_picker
from pyFAI.peak_picker import PeakPicker
except ImportError:
NO_PEAK_PICKER = True
import pyFAI.geometryRefinement
from pyFAI.calibrant import Calibrant
from pyFAI.geometryRefinement import GeometryRefinement
if logger.getEffectiveLevel() <= logging.INFO:
import pylab
@unittest.skipIf(NO_PEAK_PICKER, "cannot import peak_peaker")
class test_peak_picking(unittest.TestCase):
"""basic test"""
calibFile = "1788/moke.tif"
# gr = GeometryRefinement()
ctrlPt = {0:(300, 230),
1:(300, 212),
2:(300, 195),
3:(300, 177),
4:(300, 159),
5:(300, 140),
6:(300, 123),
7:(300, 105),
8:(300, 87)}
tth = numpy.radians(numpy.arange(4, 13))
wavelength = 1e-10
ds = wavelength * 5e9 / numpy.sin(tth / 2)
calibrant = Calibrant(dSpacing=ds)
maxiter = 100
tmp_dir = os.environ.get("PYFAI_TEMPDIR", os.path.join(os.path.dirname(os.path.abspath(__file__)), "tmp"))
logfile = os.path.join(tmp_dir, "testpeakPicking.log")
nptfile = os.path.join(tmp_dir, "testpeakPicking.npt")
def setUp(self):
"""Download files"""
self.img = UtilsTest.getimage(self.__class__.calibFile)
self.pp = PeakPicker(self.img, calibrant=self.calibrant, wavelength=self.wavelength)
if not os.path.isdir(self.tmp_dir):
os.makedirs(self.tmp_dir)
if os.path.isfile(self.logfile):
os.unlink(self.logfile)
if os.path.isfile(self.nptfile):
os.unlink(self.nptfile)
def tearDown(self):
"""Remove temporary files"""
unittest.TestCase.tearDown(self)
if os.path.isfile(self.logfile):
os.unlink(self.logfile)
if os.path.isfile(self.nptfile):
os.unlink(self.nptfile)
def test_peakPicking(self):
"""first test peak-picking then checks the geometry found is OK"""
for i in self.ctrlPt:
pts = self.pp.massif.find_peaks(self.ctrlPt[i], stdout=open(self.logfile, "a"))
logger.info("point %s at ring #%i (tth=%.1f deg) generated %i points", self.ctrlPt[i], i, self.tth[i], len(pts))
if len(pts) > 0:
self.pp.points.append(pts, ring=i)
else:
logger.error("point %s caused error (%s) ", i, self.ctrlPt[i])
self.pp.points.save(self.nptfile)
lstPeak = self.pp.points.getListRing()
# print self.pp.points
# print lstPeak
logger.info("After peak-picking, we have %s points generated from %s groups ", len(lstPeak), len(self.ctrlPt))
gr = GeometryRefinement(lstPeak, dist=0.01, pixel1=1e-4, pixel2=1e-4, wavelength=self.wavelength, calibrant=self.calibrant)
gr.guess_poni()
logger.info(gr.__repr__())
last = sys.maxint
for i in range(self.maxiter):
delta2 = gr.refine2()
logger.info(gr.__repr__())
if delta2 == last:
logger.info("refinement finished after %s iteration" % i)
break
last = delta2
self.assertEquals(last < 1e-4, True, "residual error is less than 1e-4, got %s" % last)
self.assertAlmostEquals(gr.dist, 0.1, 2, "distance is OK, got %s, expected 0.1" % gr.dist)
self.assertAlmostEquals(gr.poni1, 3e-2, 2, "PONI1 is OK, got %s, expected 3e-2" % gr.poni1)
self.assertAlmostEquals(gr.poni2, 3e-2, 2, "PONI2 is OK, got %s, expected 3e-2" % gr.poni2)
self.assertAlmostEquals(gr.rot1, 0, 2, "rot1 is OK, got %s, expected 0" % gr.rot1)
self.assertAlmostEquals(gr.rot2, 0, 2, "rot2 is OK, got %s, expected 0" % gr.rot2)
self.assertAlmostEquals(gr.rot3, 0, 2, "rot3 is OK, got %s, expected 0" % gr.rot3)
# print self.pp.points
class test_Massif(unittest.TestCase):
"""test for ring extraction algorithm with image which needs binning (non regression test)"""
calibFile = "1788/moke.tif"
def test_suite_all_PeakPicking():
testSuite = unittest.TestSuite()
testSuite.addTest(test_peak_picking("test_peakPicking"))
return testSuite
if __name__ == '__main__':
mysuite = test_suite_all_PeakPicking()
runner = unittest.TextTestRunner()
runner.run(mysuite)
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