Currently job artifacts in CI/CD pipelines on LRZ GitLab never expire. Starting from Wed 26.1.2022 the default expiration time will be 30 days (GitLab default). Currently existing artifacts in already completed jobs will not be affected by the change. The latest artifacts for all jobs in the latest successful pipelines will be kept. More information: https://gitlab.lrz.de/help/user/admin_area/settings/continuous_integration.html#default-artifacts-expiration

csvdimagereader.cpp 7.77 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
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
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
// ================================================================================================
// 
// This file is part of the CAMPVis Software Framework.
// 
// If not explicitly stated otherwise: Copyright (C) 2012, all rights reserved,
//      Christian Schulte zu Berge <christian.szb@in.tum.de>
//      Chair for Computer Aided Medical Procedures
//      Technische Universitt Mnchen
//      Boltzmannstr. 3, 85748 Garching b. Mnchen, Germany
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
// 
// The licensing of this softare is not yet resolved. Until then, redistribution in source or
// binary forms outside the CAMP chair is not permitted, unless explicitly stated in legal form.
// However, the names of the original authors and the above copyright notice must retain in its
// original state in any case.
// 
// Legal disclaimer provided by the BSD license:
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY 
// AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR 
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR 
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
// 
// ================================================================================================

#include "csvdimagereader.h"

#include <iostream>
#include <fstream>
#include <sstream>
#include <string>

#include "tgt/filesystem.h"
#include "core/datastructures/imagedata.h"
#include "core/datastructures/imagerepresentationdisk.h"
#include "core/datastructures/genericimagerepresentationlocal.h"
#include "core/tools/textfileparser.h"

namespace campvis {
    const std::string CsvdImageReader::loggerCat_ = "CAMPVis.modules.io.CsvdImageReader";

    CsvdImageReader::CsvdImageReader() 
        : AbstractProcessor()
        , p_url("url", "Image URL", "")
        , p_targetImageID("targetImageName", "Target Image ID", "CsvdImageReader.output", DataNameProperty::WRITE)
        , p_imageOffset("ImageOffset", "Image Offset in mm", tgt::vec3(0.f), tgt::vec3(-10000.f), tgt::vec3(10000.f))
        , p_voxelSize("VoxelSize", "Voxel Size in mm", tgt::vec3(1.f), tgt::vec3(-100.f), tgt::vec3(100.f))
    {
        addProperty(&p_url);
        addProperty(&p_targetImageID);
        addProperty(&p_imageOffset);
        addProperty(&p_voxelSize);
    }

    CsvdImageReader::~CsvdImageReader() {

    }

    void CsvdImageReader::process(DataContainer& data) {
        try {
            // start parsing
            TextFileParser tfp(p_url.getValue(), true, "=");
            tfp.parse<TextFileParser::ItemSeparatorLines>();

            // init optional parameters with sane default values
            size_t dimensionality = 3;
            tgt::svec3 size;
            WeaklyTypedPointer::BaseType pt;
            size_t numChannels = 1;

            tgt::vec3 voxelSize(1.f);
            tgt::vec3 imageOffset(0.f);

            // dimensionality and size
            if (tfp.hasKey("Size")) {
                size = tfp.getSvec3("Size");
            }
            else {
                LERROR("Error while parsing CSVD header: No Size specified.");
                return;
            }

            // element type
            std::string et = tfp.getString("ElementType");
            if (et == "UINT8")
                pt = WeaklyTypedPointer::UINT8;
            else if (et == "INT8")
                pt = WeaklyTypedPointer::INT8;
            else if (et == "UINT16")
                pt = WeaklyTypedPointer::UINT16;
            else if (et == "INT16")
                pt = WeaklyTypedPointer::INT16;
            else if (et == "UINT32")
                pt = WeaklyTypedPointer::UINT32;
            else if (et == "INT32")
                pt = WeaklyTypedPointer::INT32;
            else if (et == "FLOAT")
                pt = WeaklyTypedPointer::FLOAT;
            else {
                LERROR("Error while parsing MHD header: Unsupported element type: " << et);
                return;
            }

            // dimensionality and size
            if (tfp.hasKey("CsvFileBaseName")) {
                ImageData* image = new ImageData(dimensionality, size, 1);
                ImageRepresentationLocal* rep = 0;
                size_t index = 0;

                std::string url = StringUtils::trim(tfp.getString("CsvFileBaseName"));
                url = tgt::FileSystem::cleanupPath(tgt::FileSystem::dirName(p_url.getValue()) + "/" + url);

                // start parsing of CSV files
#define DISPATCH_PARSING(WTP_TYPE, C_TYPE, TMP_TYPE) \
    if (pt == WTP_TYPE) {\
        C_TYPE* dataArray = new C_TYPE[tgt::hmul(size)]; \
        for (size_t slice = 0; slice < size.z; ++slice) { \
            std::stringstream ss; \
            ss << url << slice << ".csv"; \
            std::string concatenated = ss.str(); \
             \
            std::ifstream file(concatenated.c_str(), std::ifstream::in); \
            if (!file.is_open() || file.bad()) \
                throw tgt::FileException("Could not open file " + ss.str() + " for reading.", p_url.getValue()); \
                 \
            TMP_TYPE tmp; \
            for (size_t column = 0; column < size.y; ++column) { \
                for (size_t row = 0; row < size.x && file.good(); ++row) { \
                    file >> tmp; \
                    dataArray[index++] = static_cast<C_TYPE>(tmp); \
                    file.get(); /* TODO: simple hack to advance to next character - but there might be more than one... */ \
                } \
            } \
        } \
        rep = GenericImageRepresentationLocal<C_TYPE, 1>::create(image, dataArray); \
    }

                DISPATCH_PARSING(WeaklyTypedPointer::UINT8      , uint8_t, uint16_t)
                else DISPATCH_PARSING(WeaklyTypedPointer::INT8  , int8_t, int16_t)
                else DISPATCH_PARSING(WeaklyTypedPointer::UINT16, uint16_t, uint16_t)
                else DISPATCH_PARSING(WeaklyTypedPointer::INT16 , int16_t, int16_t)
                else DISPATCH_PARSING(WeaklyTypedPointer::UINT32, uint32_t, uint32_t)
                else DISPATCH_PARSING(WeaklyTypedPointer::INT32 , int32_t, int32_t)
                else DISPATCH_PARSING(WeaklyTypedPointer::FLOAT , float, float)
                
                if (rep != 0) {
                    // all parsing done - lets create the image:
                    image->setMappingInformation(ImageMappingInformation(size, imageOffset + p_imageOffset.getValue(), voxelSize + p_voxelSize.getValue()));
                    data.addData(p_targetImageID.getValue(), image);
                    p_targetImageID.issueWrite();
                }
                else {
                    throw tgt::FileException("Error while parsing the data.", p_url.getValue());
                }
            }
            else {
                LERROR("Error while parsing CSVD header: No file names specified.");
                return;
            }
        }
        catch (tgt::Exception& e) {
            LERROR("Error while parsing MHD header: " << e.what());
            return;
        }
        catch (std::exception& e) {
            LERROR("Error while parsing MHD header: " << e.what());
            return;
        }

174
        validate(INVALID_RESULT);
175
176
    }
}