ProteoWizard
SpectrumList_3D_Test.cpp
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1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
6//
7// Copyright 2008 Vanderbilt University - Nashville, TN 37232
8//
9// Licensed under the Apache License, Version 2.0 (the "License");
10// you may not use this file except in compliance with the License.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
27#include "SpectrumList_3D.hpp"
28#include "boost/foreach_field.hpp"
29
30using namespace pwiz::util;
31using namespace pwiz::cv;
32using namespace pwiz::msdata;
33using namespace pwiz::analysis;
34
35ostream* os_ = 0;
36
37template<typename MapT>
38typename MapT::const_iterator find_nearest(MapT const& m, typename MapT::key_type const& query, typename MapT::key_type const& tolerance)
39{
40 typename MapT::const_iterator cur, min, max, best;
41
42 min = m.lower_bound(query - tolerance);
43 max = m.lower_bound(query + tolerance);
44
45 if (min == m.end() || fabs(query - min->first) > tolerance)
46 return m.end();
47 else if (min == max)
48 return min;
49 else
50 best = min;
51
52 double minDiff = fabs(query - best->first);
53 for (cur = min; cur != max; ++cur)
54 {
55 double curDiff = fabs(query - cur->first);
56 if (curDiff < minDiff)
57 {
58 minDiff = curDiff;
59 best = cur;
60 }
61 }
62 return best;
63}
64
65
66// drift time
67// m/z 100 200 300 400 500 600
68// 123.4 0 1 2 1 0 0
69// 234.5 1 2 3 2 1 0
70// 345.6 2 3 4 3 2 1
71// 456.7 1 2 3 2 1 0
72// 567.8 0 1 2 1 0 0
73// translates to:
74// "100,123.4,0 200,123.4,1 300,123.4,2 400,123.4,1 500,123.4,0 600,123.4,0 100,234.5,1 200,123.4,2 300,123.4,3 400,123.4,2 500,123.4,1 600,123.4,0 etc."
75
76void test(const MSDataFile& msd, double scanStartTime, const char* driftTimeRanges, const char* expectedSpectrumTable)
77{
78 boost::icl::interval_set<double> driftTimeRangesSet;
79 vector<string> tokens, tokens2;
80 bal::split(tokens, driftTimeRanges, bal::is_any_of(" "));
81 BOOST_FOREACH(const string& token, tokens)
82 {
83 bal::split(tokens2, token, bal::is_any_of("-"));
84 driftTimeRangesSet.add(boost::icl::continuous_interval<double>(lexical_cast<double>(tokens2[0]), lexical_cast<double>(tokens2[1])));
85 }
86
87 Spectrum3D expectedSpectrum3d;
88 bal::split(tokens, expectedSpectrumTable, bal::is_any_of(" "));
89 BOOST_FOREACH(const string& token, tokens)
90 {
91 bal::split(tokens2, token, bal::is_any_of(","));
92 expectedSpectrum3d[lexical_cast<double>(tokens2[0])][lexical_cast<double>(tokens2[1])] = lexical_cast<double>(tokens2[2]);
93 }
94
96 Spectrum3DPtr resultSpectrum3d = sl.spectrum3d(scanStartTime, driftTimeRangesSet);
97
98 unit_assert(!resultSpectrum3d->empty());
99 Spectrum3D inResultButNotExpected, inExpectedButNotResult;
100 BOOST_FOREACH_FIELD((double actualDriftTime)(const Spectrum3D::value_type::second_type& resultSpectrum), *resultSpectrum3d)
101 BOOST_FOREACH_FIELD((double expectedDriftTime)(const Spectrum3D::value_type::second_type& expectedSpectrum), expectedSpectrum3d)
102 {
103 if (find_nearest(*resultSpectrum3d, expectedDriftTime, 1e-5) == resultSpectrum3d->end())
104 inExpectedButNotResult[expectedDriftTime] = Spectrum3D::value_type::second_type();
105 if (find_nearest(expectedSpectrum3d, actualDriftTime, 1e-5) == expectedSpectrum3d.end())
106 inResultButNotExpected[actualDriftTime] = Spectrum3D::value_type::second_type();
107
108 if (fabs(actualDriftTime - expectedDriftTime) < 1e-5)
109 BOOST_FOREACH_FIELD((double actualMz)(double actualIntensity), resultSpectrum)
110 BOOST_FOREACH_FIELD((double expectedMz)(double expectedIntensity), expectedSpectrum)
111 {
112 if (find_nearest(resultSpectrum, expectedMz, 1e-4) == resultSpectrum.end())
113 inExpectedButNotResult[expectedDriftTime][expectedMz] = expectedIntensity;
114 if (find_nearest(expectedSpectrum, actualMz, 1e-4) == expectedSpectrum.end())
115 inResultButNotExpected[actualDriftTime][actualMz] = actualIntensity;
116 }
117 }
118
119 if (os_ && !inResultButNotExpected.empty())
120 {
121 *os_ << "Extra points in the result were not expected:\n";
122 BOOST_FOREACH_FIELD((double driftTime)(const Spectrum3D::value_type::second_type& spectrum), inResultButNotExpected)
123 {
124 *os_ << driftTime << ":";
125 BOOST_FOREACH_FIELD((double mz)(double intensity), spectrum)
126 *os_ << " " << mz << "," << intensity;
127 *os_ << endl;
128 }
129 }
130
131 if (os_ && !inExpectedButNotResult.empty())
132 {
133 *os_ << "Missing points in the result that were expected:\n";
134 BOOST_FOREACH_FIELD((double driftTime)(const Spectrum3D::value_type::second_type& spectrum), inExpectedButNotResult)
135 {
136 *os_ << driftTime << ":";
137 BOOST_FOREACH_FIELD((double mz)(double intensity), spectrum)
138 *os_ << " " << mz << "," << intensity;
139 *os_ << endl;
140 }
141 }
142
143 unit_assert(inResultButNotExpected.empty());
144 unit_assert(inExpectedButNotResult.empty());
145}
146
147
148void parseArgs(const vector<string>& args, vector<string>& rawpaths)
149{
150 for (size_t i = 1; i < args.size(); ++i)
151 {
152 if (args[i] == "-v") os_ = &cout;
153 else if (bal::starts_with(args[i], "--")) continue;
154 else rawpaths.push_back(args[i]);
155 }
156}
157
158
159int main(int argc, char* argv[])
160{
161 TEST_PROLOG(argc, argv)
162
163 try
164 {
165 vector<string> args(argv, argv+argc);
166 vector<string> rawpaths;
167 parseArgs(args, rawpaths);
168
169 ExtendedReaderList readerList;
170
171 BOOST_FOREACH(const string& filepath, rawpaths)
172 {
173 if (bal::ends_with(filepath, "ImsSynthCCS.d"))
174 {
175 MSDataFile msd(filepath, &readerList);
176 // scans 529, 554, 557, 615, 638
177 test(msd, 4.2, "29.6-29.7 33.8-33.9 34.4-34.41 34.57-34.58 44.23-44.24 48.13-48.14",
178 "33.89830,99.9954,0 34.57627,99.9954,0 29.66101,99.9954,0 34.40678,99.9954,0 44.23729,99.9954,0 48.13559,99.9954,0 " // I don't know why these isolated points show up
179 "33.89830,174.03522,0 33.89830,174.04278,1 33.89830,174.05034,1 33.89830,174.05790,1 33.89830,174.06546,1 33.89830,174.07302,0 33.89830,174.35288,0 33.89830,174.36044,1 "
180 "33.89830,174.36801,1 33.89830,174.37558,1 33.89830,174.38314,1 33.89830,174.39071,1 33.89830,174.39828,1 33.89830,174.40585,1 33.89830,174.41342,1 34.57627,177.05704,0 "
181 "34.57627,177.06466,1 34.57627,177.07229,1 34.57627,177.07991,1 34.57627,177.08754,2 34.40678,177.09517,0 34.57627,177.09517,3 34.40678,177.10279,1 34.57627,177.10279,3 "
182 "34.40678,177.11042,1 34.57627,177.11042,4 34.40678,177.11804,1 34.57627,177.11804,4 34.40678,177.12567,1 34.57627,177.12567,5 34.40678,177.13330,1 34.57627,177.13330,5 "
183 "34.40678,177.14092,1 34.57627,177.14092,5 34.40678,177.14855,1 34.57627,177.14855,4 34.40678,177.15618,1 34.57627,177.15618,4 34.40678,177.16381,0 34.57627,177.16381,3 "
184 "34.57627,177.17143,2 34.57627,177.17906,1 34.57627,177.18669,1 34.57627,177.19432,1 34.57627,177.20195,0 34.57627,177.59120,0 34.57627,177.59884,1 34.57627,177.60648,1 "
185 "34.57627,177.61411,1 34.57627,177.62175,1 34.57627,177.62939,1 34.57627,177.63703,1 34.57627,177.64466,1 34.57627,177.65230,1 34.57627,177.65994,1 34.57627,177.66758,1 "
186 "34.57627,177.67522,0 29.66101,177.71341,0 29.66101,177.72105,1 29.66101,177.72869,1 29.66101,177.73633,1 29.66101,177.74397,2 29.66101,177.75161,2 29.66101,177.75925,3 "
187 "29.66101,177.76689,4 29.66101,177.77453,4 29.66101,177.78217,4 29.66101,177.78981,4 29.66101,177.79745,4 29.66101,177.80509,4 29.66101,177.81274,3 29.66101,177.82038,3 "
188 "29.66101,177.82802,2 29.66101,177.83566,1 29.66101,177.84330,1 29.66101,177.85094,1 29.66101,177.85859,0 29.66101,178.07264,0 29.66101,178.08029,1 29.66101,178.08793,1 "
189 "29.66101,178.09558,1 29.66101,178.10323,1 29.66101,178.11088,1 34.57627,178.11088,0 29.66101,178.11852,2 34.57627,178.11852,1 29.66101,178.12617,1 34.57627,178.12617,1 "
190 "29.66101,178.13382,1 34.57627,178.13382,1 29.66101,178.14147,1 34.57627,178.14147,1 29.66101,178.14912,1 34.57627,178.14912,0 29.66101,178.15677,1 29.66101,178.16442,1 "
191 "29.66101,178.17206,0 29.66101,178.39396,0 29.66101,178.40161,1 29.66101,178.40927,1 29.66101,178.41692,1 29.66101,178.42458,1 29.66101,178.43223,2 29.66101,178.43989,2 "
192 "29.66101,178.44754,2 29.66101,178.45520,2 29.66101,178.46285,2 29.66101,178.47051,2 29.66101,178.47816,1 29.66101,178.48582,1 29.66101,178.49347,1 29.66101,178.50113,1 "
193 "29.66101,178.50879,0 29.66101,178.76154,0 29.66101,178.76920,1 29.66101,178.77686,1 29.66101,178.78452,1 29.66101,178.79219,1 29.66101,178.79985,1 29.66101,178.80751,1 "
194 "34.57627,398.99589,0 34.57627,399.00734,1 34.57627,399.01878,1 34.57627,399.03023,1 34.57627,399.04168,1 34.57627,399.05313,2 34.40678,399.06457,0 34.57627,399.06457,2 "
195 "34.40678,399.07602,1 34.57627,399.07602,3 34.40678,399.08747,1 34.57627,399.08747,4 34.40678,399.09892,1 34.57627,399.09892,5 34.40678,399.11036,1 34.57627,399.11036,5 "
196 "34.40678,399.12181,1 34.57627,399.12181,6 34.40678,399.13326,1 34.57627,399.13326,7 34.40678,399.14471,1 34.57627,399.14471,7 34.40678,399.15616,1 34.57627,399.15616,7 "
197 "34.40678,399.16761,1 34.57627,399.16761,7 34.40678,399.17906,1 34.57627,399.17906,7 34.40678,399.19051,1 34.57627,399.19051,7 34.40678,399.20196,1 34.57627,399.20196,7 "
198 "34.40678,399.21341,1 34.57627,399.21341,6 34.40678,399.22486,1 34.57627,399.22486,5 34.40678,399.23631,1 34.57627,399.23631,5 34.40678,399.24776,1 34.57627,399.24776,4 "
199 "34.40678,399.25921,1 34.57627,399.25921,3 34.57627,399.27066,2 34.57627,399.28211,2 34.57627,399.29356,1 34.57627,399.30501,1 34.57627,399.31646,1 34.57627,399.32791,1 "
200 "34.57627,399.33936,0 34.57627,400.04968,0 34.57627,400.06114,1 34.57627,400.07260,1 34.57627,400.08406,1 34.57627,400.09552,1 34.57627,400.10699,1 34.57627,400.11845,1 "
201 "34.57627,400.12991,2 34.57627,400.14138,2 34.57627,400.15284,2 34.57627,400.16430,2 34.57627,400.17577,2 34.57627,400.18723,2 34.57627,400.19869,2 34.57627,400.21016,2 "
202 "34.57627,400.22162,1 34.57627,400.23309,1 34.57627,400.24455,1 34.57627,400.25601,1 34.57627,400.26748,1 34.57627,400.27894,1 48.13559,608.09487,0 48.13559,608.10900,1 "
203 "44.23729,608.12313,0 48.13559,608.12313,1 44.23729,608.13726,1 48.13559,608.13726,1 44.23729,608.15139,1 48.13559,608.15139,1 44.23729,608.16553,1 48.13559,608.16553,1 "
204 "44.23729,608.17966,1 48.13559,608.17966,1 44.23729,608.19379,1 48.13559,608.19379,1 44.23729,608.20792,1 48.13559,608.20792,1 44.23729,608.22206,1 48.13559,608.22206,1 "
205 "44.23729,608.23619,1 48.13559,608.23619,2 44.23729,608.25032,1 48.13559,608.25032,2 44.23729,608.26445,1 48.13559,608.26445,2 44.23729,608.27859,1 48.13559,608.27859,2 "
206 "44.23729,608.29272,1 48.13559,608.29272,2 44.23729,608.30685,1 48.13559,608.30685,2 44.23729,608.32099,1 48.13559,608.32099,2 44.23729,608.33512,1 48.13559,608.33512,1 "
207 "44.23729,608.34926,1 48.13559,608.34926,1 44.23729,608.36339,1 48.13559,608.36339,1 44.23729,608.37753,1 48.13559,608.37753,1 44.23729,608.39166,1 48.13559,608.39166,1 "
208 "44.23729,608.40579,1 48.13559,608.40579,1 48.13559,608.41993,1 48.13559,608.43406,1 48.13559,608.44820,0 48.13559,609.19760,0 48.13559,609.21175,1 48.13559,609.22589,1 "
209 "48.13559,609.24004,1 48.13559,609.25418,1 48.13559,609.26832,1 48.13559,609.28247,1 48.13559,609.29661,1 48.13559,609.31076,1 48.13559,609.32491,1 48.13559,609.33905,1");
210 }
211 // TODO: add a Waters test
212 /*else if (bal::ends_with(filepath, "GFP_IMS_TEST.raw"))
213 {
214 MSDataFile msd(filepath, &readerList);
215 // scans 529, 554, 557, 615, 638
216 test(msd, 2.03500008, "13.29-13.30 13.22-13.23 13.15-13.16",
217 "13.15698,1,0 13.22623,1,0 13.29547,1,0");
218 }*/
219 }
220 }
221 catch (exception& e)
222 {
223 TEST_FAILED(e.what())
224 }
225 catch (...)
226 {
227 TEST_FAILED("Caught unknown exception.")
228 }
229
231}
int main(int argc, char *argv[])
MapT::const_iterator find_nearest(MapT const &m, typename MapT::key_type const &query, typename MapT::key_type const &tolerance)
ostream * os_
void parseArgs(const vector< string > &args, vector< string > &rawpaths)
SpectrumList implementation that can create 3D spectra of ion mobility drift time and m/z.
virtual Spectrum3DPtr spectrum3d(double scanStartTime, const boost::icl::interval_set< double > &driftTimeRanges) const
creates a 3d spectrum at the given scan start time (specified in seconds) and including the given dri...
default ReaderList, extended to include vendor readers
boost::shared_ptr< Spectrum3D > Spectrum3DPtr
boost::container::flat_map< double, boost::container::flat_map< double, float > > Spectrum3D
MSData object plus file I/O.
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
Definition MSData.hpp:886
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here....
Definition MSData.hpp:827
#define unit_assert(x)
Definition unit.hpp:85
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175