Package pymontecarlo.util.hdf5

Examples of pymontecarlo.util.hdf5.HDF5Attribute

79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
        super.saveResults(root, key);

        HDF5Group group = root.requireSubgroup(key);

        String transitionName;
        HDF5Dataset ds;
        int[][] emptyData = new int[][] { { 0 } };
        for (XRayTransition transition : transitions) {
            transitionName = transition.getIUPACName();

            ds = group.createDataset(transitionName, emptyData);

            ds.setAttribute("gnf", gnfIntensities.get(transition), 0.0);
            ds.setAttribute("enf", enfIntensities.get(transition), 0.0);
            ds.setAttribute("et", etIntensities.get(transition), 0.0);
        }
    }
View Full Code Here
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
        Trajectory trajectory;
        String name;
        double[][] data;
        int interactionsSize;
        Double[] interaction;
        HDF5Dataset dataset;
        for (int i = 0; i < trajectories.size(); i++) {
            trajectory = trajectories.get(i);

            name = "trajectory" + i;

            interactionsSize = trajectory.interactions.size();
            data = new double[interactionsSize][6];
            for (int j = 0; j < interactionsSize; j++) {
                interaction = trajectory.interactions.get(j);
                data[j][0] = interaction[0];
                data[j][1] = interaction[1];
                data[j][2] = interaction[2];
                data[j][3] = interaction[3];
                data[j][4] = interaction[4];
                data[j][5] = interaction[5];
            }

            dataset = group.createDataset(name, data);

            dataset.setAttribute("primary", trajectory.primary ? 1 : 0);
            dataset.setAttribute("particle", 1); // Electron
            dataset.setAttribute("collision", trajectory.collision);
            dataset.setAttribute("exit_state", trajectory.exitState);
        }
    }
View Full Code Here
91
92
93
94
95
96
97
98
99
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
        HDF5Group group = root.requireSubgroup(key);

        double normFactor = (double) trajectoryCount;

        String transitionName;
        HDF5Dataset ds;
        double gcf, gbf, gnf;
        double ecf, ebf, enf;
        int[][] emptyData = new int[][] { { 0 } };
        for (XRayTransition transition : accumCharac.getTransitions()) {
            transitionName = transition.getIUPACName();

            ds = group.createDataset(transitionName, emptyData);

            gnf = accumCharac.getGenerated(transition) / normFactor;
            enf = accumCharac.getEmitted(transition) / normFactor;

            gcf = ecf = 0.0;
            if (accumCharacFluo != null) {
                gcf = accumCharacFluo.getGenerated(transition) / normFactor;
                ecf = accumCharacFluo.getEmitted(transition) / normFactor;
            }

            gbf = ebf = 0.0;
            if (accumBremssFluo != null) {
                gbf = accumBremssFluo.getGenerated(transition) / normFactor;
                ebf = accumBremssFluo.getEmitted(transition) / normFactor;
            }

            ds.setAttribute("gcf", gcf, 0.0);
            ds.setAttribute("gbf", gbf, 0.0);
            ds.setAttribute("gnf", gnf, 0.0);
            ds.setAttribute("gt", gnf + gcf + gbf, 0.0);

            ds.setAttribute("ecf", ecf, 0.0);
            ds.setAttribute("ebf", ebf, 0.0);
            ds.setAttribute("enf", enf, 0.0);
            ds.setAttribute("et", enf + ecf + ebf, 0.0);
        }
    }
View Full Code Here
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53


    @Override
    public void saveResults(HDF5Group root, String key) throws IOException {
        HDF5Group group = root.requireSubgroup(key);

        // Set Python class
        group.setAttribute("_class", getPythonResultClass());

        // Save log
        Properties props = new Properties();
        createLog(props);
        group.setAttribute("log", props.toString());
    }
View Full Code Here
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
    @Override
    public void saveResults(HDF5Group root, String key) throws IOException {
        super.saveResults(root, key);

        HDF5Group group = root.requireSubgroup(key);

        String transitionName;
        HDF5Dataset ds;
        int[][] emptyData = new int[][] { { 0 } };
        for (XRayTransition transition : transitions) {
            transitionName = transition.getIUPACName();

            ds = group.createDataset(transitionName, emptyData);

            ds.setAttribute("gnf", gnfIntensities.get(transition), 0.0);
            ds.setAttribute("enf", enfIntensities.get(transition), 0.0);
            ds.setAttribute("et", etIntensities.get(transition), 0.0);
        }
View Full Code Here
105
106
107
108
109
110
111
112
113
114
115
            mcss.runTrajectory();
        }

        // Save results
        report(1.0, "Saving results");
        HDF5Group rootGroup =
                createHDF5Group(mcss, detectors, rootElement, name);
        File resultsH5 = new File(resultsDir, name + ".h5");
        HDF5FileWriter.write(rootGroup, resultsH5, true);

        report(1.0, "Complete");
View Full Code Here
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287

    private HDF5Group createHDF5Group(MonteCarloSS mcss,
            Map<String, Detector> detectors,
            Element rootElement, String name) throws IOException {
        HDF5Group rootGroup = HDF5Group.createRoot();

        // Save version, class
        rootGroup.setAttribute("version", VERSION);
        rootGroup.setAttribute("_class", "Results");

        // Create results group
        String identifier = rootElement.getAttributeValue("uuid");
        rootGroup.setAttribute("identifiers", new String[] { identifier });

        HDF5Group resultsGroup =
                rootGroup.createSubgroup("result-" + identifier);

        // Save results from detectors
        String key;
        Detector detector;
        for (Entry<String, Detector> entry : detectors.entrySet()) {
            key = entry.getKey();
            detector = entry.getValue();

            detector.saveResults(resultsGroup, key);
        }

        // Save overall log
        Properties props = new Properties();
        createLog(props, mcss);
        resultsGroup.setAttribute("log", props.toString());

        // Save options
        XMLOutputter outputter = new XMLOutputter(Format.getCompactFormat());
        String optionsStr = outputter.outputString(rootElement);
        resultsGroup.setAttribute("options", optionsStr);
        rootGroup.setAttribute("options", optionsStr);

        return rootGroup;
    }
View Full Code Here
35
36
37
38
39
40
41
42
43


    @Test
    public void testSaveResults() throws Exception {
        HDF5Group root = HDF5Group.createRoot();
        det.saveResults(root, "det1");
        HDF5FileWriter.write(root, resultsFile, true);
    }
View Full Code Here
43
44
45
46
47
48
49
50
51


    @Test
    public void testSaveResults() throws IOException {
        HDF5Group root = HDF5Group.createRoot();
        det.saveResults(root, "det1");
        HDF5FileWriter.write(root, resultsFile, true);
    }
View Full Code Here
138
139
140
141
142
143
144
145
146
147
        double[][] spectrumTotal =
                arrayFromSpectrum(detectorTotal.getSpectrum(1.0));
        double[][] spectrumBackground =
                arrayFromSpectrum(detectorBackground.getSpectrum(1.0));

        HDF5Group group = root.requireSubgroup(key);

        group.createDataset("total", spectrumTotal);
        group.createDataset("background", spectrumBackground);
    }
View Full Code Here
TOP

Related Classes of pymontecarlo.util.hdf5.HDF5Attribute

  • edu.ucar.ral.nujan.hdf.HdfFileWriter
  • edu.ucar.ral.nujan.hdf.HdfGroup
  • pymontecarlo.program._analytical.AbstractAnalyticalWorker
  • pymontecarlo.program._analytical.options.detector.AbstractDetector
  • pymontecarlo.program._analytical.options.detector.PhiZDetector
  • pymontecarlo.program._analytical.options.detector.PhotonIntensityDetector
  • pymontecarlo.program.nistmonte.options.detector.AbstractDetector
  • pymontecarlo.program.nistmonte.options.detector.AbstractPhotonDetectorTest
  • pymontecarlo.program.nistmonte.options.detector.BackscatteredElectronRadialDetector
  • pymontecarlo.program.nistmonte.options.detector.PhiZDetector
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.