├── .gitignore ├── COPYING ├── README.md ├── RVElogoclearback-80.png ├── RhizoVisionExplorer-window.png ├── RhizoVisionExplorer.sln ├── RhizoVisionExplorer ├── MainUI.cpp ├── MainUI.h ├── RhizoVisionExplorer.json ├── RhizoVisionExplorer.rc ├── RhizoVisionExplorer.vcxproj ├── RhizoVisionExplorer.vcxproj.filters ├── RhizoVisionExplorer.vcxproj.user ├── common_types.h ├── demo.h ├── icons │ ├── RVElogoclearback-150.png │ ├── RVElogoclearback.png │ └── rveicon.ico ├── main.cpp ├── moc_FeatureExtractorThread.cpp ├── moc_MainUI.cpp ├── qrc_resources.cpp ├── resource.h ├── resources.qrc ├── rootsegmentprop.cpp ├── rootsegmentprop.h ├── roottopology.cpp └── roottopology.h └── changelog.txt /.gitignore: -------------------------------------------------------------------------------- 1 | # Prerequisites 2 | *.d 3 | 4 | # Compiled Object files 5 | *.slo 6 | *.lo 7 | *.o 8 | *.obj 9 | 10 | # Precompiled Headers 11 | *.gch 12 | *.pch 13 | 14 | # Compiled Dynamic libraries 15 | *.so 16 | *.dylib 17 | *.dll 18 | 19 | # Fortran module files 20 | *.mod 21 | *.smod 22 | 23 | # Compiled Static libraries 24 | *.lai 25 | *.la 26 | *.a 27 | *.lib 28 | 29 | # Executables 30 | *.exe 31 | *.out 32 | *.app 33 | -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # ![RhiZoVision Explorer Logo](./RVElogoclearback-80.png) RhizoVision Explorer 2 | 3 | RhizoVision Explorer is free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera. Root images are expected to have a high contrast of roots with the background, homogenous lighting, and minimal overlapping of roots. The software is built in C++ for speed and stability, using QT for the graphical user interface and OpenCV for image processing. Traits extracted by RhizoVision Explorer have been extensively validated using a physical copper wire ground truth image set, thousands of simulated roots, and comparisons with other image analysis software. The default “Broken Roots” mode is meant for roots washed out from soil cores or pots that are disconnected and provides length, volume, branching frequency, among other features, with the ability to bin measurements based on diameter thresholds. The “Whole Root” mode extracts additional root system architecture features of more intact root systems, especially excavated root crowns or rhizoboxes, such as the convex hull, angles, and holes. The software supports multiple regions of interest, batch mode, and user-defined export of processed images with overlaid features for use in reports. 4 | 5 | #### Downloading 6 | The software binary can be downloaded [here](https://doi.org/10.5281/zenodo.3747697). 7 | 8 | The source code repository is located [here](https://github.com/rootphenomicslab/RhizoVisionExplorer). 9 | 10 | #### Running the Program 11 | 12 | The program opens a GUI where we specify the location of root images and output location to save the processed images and the extracted features. We can change the options that suit the input images and click the start button to start extracting the feature traits from the root images. 13 | 14 | ![](./RhizoVisionExplorer-window.png) 15 | 16 | #### Pre-requisites for Running the Program 17 | 18 | This program needs an x86_64 processor. Any Intel or AMD processor may be used for running the program. If the CPU supports Intel AVX 2.0, the program runs faster for feature extraction. 19 | 20 | #### Compiling the Source 21 | 22 | The source code is compiled using Microsoft Visual Studio. The program depends on Qt 5.12.3, OpenCV 4.1 and [cvutil](https://github.com/rootphenomicslab/cvutil) 2.0.3 libraries for compiling the source. 23 | 24 | #### Copyright and License 25 | 26 | Copyright (C) 2021, Anand Seethepalli and Larry York 27 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 28 | 29 | **RhizoVision Explorer** 30 | 31 | RhizoVision Explorer 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. 32 | 33 | RhizoVision Explorer 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. 34 | 35 | You should have received a copy of the GNU General Public License along with RhizoVision Explorer; see the file COPYING. If not, see . 36 | 37 | #### Citing 38 | Please use the following citation when using the software. 39 | 40 | > Anand Seethepalli, & Larry York. RhizoVision Explorer - Interactive software for generalized root image analysis designed for everyone (Version 2.0.3). Zenodo. https://doi.org/10.5281/zenodo.3747697 41 | 42 | #### Authors 43 | 44 | Please send any comments/suggestions/improvements for the program to the authors: 45 | 46 | Anand Seethepalli 47 | anand.seethepalli@yahoo.co.in 48 | 49 | Larry York 50 | larry.york@gmail.com 51 | 52 | -------------------------------------------------------------------------------- /RVElogoclearback-80.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/predictivephenomics/RhizoVisionExplorer/42750c9d238153dd2d707267c70dcbe66e302083/RVElogoclearback-80.png -------------------------------------------------------------------------------- /RhizoVisionExplorer-window.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/predictivephenomics/RhizoVisionExplorer/42750c9d238153dd2d707267c70dcbe66e302083/RhizoVisionExplorer-window.png -------------------------------------------------------------------------------- /RhizoVisionExplorer.sln: -------------------------------------------------------------------------------- 1 |  2 | Microsoft Visual Studio Solution File, Format Version 12.00 3 | # Visual Studio 14 4 | VisualStudioVersion = 14.0.25420.1 5 | MinimumVisualStudioVersion = 10.0.40219.1 6 | Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "RhizoVisionExplorer", "RhizoVisionExplorer\RhizoVisionExplorer.vcxproj", "{868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}" 7 | EndProject 8 | Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{A147851C-C2B1-4F81-8DF1-71F4D8841EA4}" 9 | ProjectSection(SolutionItems) = preProject 10 | changelog.txt = changelog.txt 11 | LICENSE = LICENSE 12 | README.md = README.md 13 | RhizoVisionExplorer-window.png = RhizoVisionExplorer-window.png 14 | RVElogoclearback-150.png = RVElogoclearback-150.png 15 | EndProjectSection 16 | EndProject 17 | Global 18 | GlobalSection(SolutionConfigurationPlatforms) = preSolution 19 | Debug|x64 = Debug|x64 20 | Debug|x86 = Debug|x86 21 | Release|x64 = Release|x64 22 | Release|x86 = Release|x86 23 | EndGlobalSection 24 | GlobalSection(ProjectConfigurationPlatforms) = postSolution 25 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Debug|x64.ActiveCfg = Debug|x64 26 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Debug|x64.Build.0 = Debug|x64 27 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Debug|x86.ActiveCfg = Debug|x64 28 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Debug|x86.Build.0 = Debug|x64 29 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Release|x64.ActiveCfg = Release|x64 30 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Release|x64.Build.0 = Release|x64 31 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Release|x86.ActiveCfg = Release|Win32 32 | {868F0440-8F50-4AAC-AEF2-C9A0AEB2635E}.Release|x86.Build.0 = Release|Win32 33 | EndGlobalSection 34 | GlobalSection(SolutionProperties) = preSolution 35 | HideSolutionNode = FALSE 36 | EndGlobalSection 37 | EndGlobal 38 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/MainUI.h: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (C) 2021, Anand Seethepalli and Larry York 3 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 4 | 5 | File: MainUI.h 6 | 7 | Authors: 8 | Anand Seethepalli (anand.seethepalli@yahoo.co.in) 9 | Larry York (larry.york@gmail.com) 10 | 11 | This file is part of RhizoVision Explorer. 12 | 13 | RhizoVision Explorer is free software: you can redistribute 14 | it and/or modify it under the terms of the GNU General Public 15 | License as published by the Free Software Foundation, either 16 | version 3 of the License, or (at your option) any later version. 17 | 18 | RhizoVision Explorer is distributed in the hope that it will 19 | be useful, but WITHOUT ANY WARRANTY; without even the implied 20 | warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 21 | PURPOSE. See the GNU General Public License for more details. 22 | 23 | You should have received a copy of the GNU General Public 24 | License along with RhizoVision Explorer; see the file COPYING. 25 | If not, see . 26 | */ 27 | 28 | #pragma once 29 | 30 | #ifndef MAINUI_H 31 | #define MAINUI_H 32 | 33 | #include 34 | #include 35 | 36 | #include 37 | #include 38 | #include 39 | #include 40 | 41 | #include 42 | #include 43 | #include 44 | 45 | //#include "FeatureExtractorThread.h" 46 | 47 | #define RHIZOVISION_EXPLORER_VERSION "2.0.3" 48 | 49 | QT_BEGIN_NAMESPACE 50 | class QAction; 51 | class QDialogButtonBox; 52 | class QGroupBox; 53 | class QLabel; 54 | class QLineEdit; 55 | class QMenu; 56 | class QMenuBar; 57 | class QPushButton; 58 | class QTextEdit; 59 | class QCheckBox; 60 | class QProgressBar; 61 | class QVBoxLayout; 62 | class QStatusBar; 63 | class QSpinBox; 64 | class QDoubleSpinBox; 65 | class QSlider; 66 | class QComboBox; 67 | QT_END_NAMESPACE 68 | 69 | class MainUI; 70 | 71 | typedef struct 72 | { 73 | cv::Mat input; 74 | cv::Mat seg; 75 | cv::Mat processed; 76 | std::vector features; 77 | std::vector rootlengthhist; 78 | std::vector> roifeatures; 79 | std::vector> roirootlengthhist; 80 | 81 | cv::Mat rtdpoints; // To get length-diameter profile 82 | 83 | int rotation = 0; 84 | 85 | // UI option for type of root being processed 86 | // 0 = Whole root 87 | // 1 = Broken roots 88 | int roottype = 1; 89 | 90 | // UI option for threshold to be applied for segmentation 91 | int threshold = 200; 92 | 93 | // UI option for image color inversion 94 | bool invertimage = false; 95 | 96 | // UI options for line smoothing 97 | bool enablesmooththresh = false; 98 | double smooththresh = 2.0; 99 | 100 | // UI options for filtering noisy components 101 | bool keepLargest = true; 102 | bool filterbknoise = false; 103 | bool filterfgnoise = false; 104 | double maxcompsizebk = 1.0; 105 | double maxcompsizefg = 1.0; 106 | 107 | // UI option for root pruning 108 | bool enableRootPruning = false; 109 | int rootPruningThreshold = 1; 110 | 111 | // UI options for convert pixels to physical units 112 | bool pixelconv = false; 113 | double conversion = 1.0; 114 | int pixelspermm = 0; // 0 for DPI, 1 for Pixels per mm 115 | 116 | // UI options for diameter ranges 117 | std::vector dranges = { 2.0, 5.0 }; 118 | 119 | // Setting to interactively change the image being shown 120 | int displayOutputIndex = 0; 121 | 122 | // UI options for displaying output options 123 | bool showConvexHull = true; // For whole root only 124 | bool showHoles = true; // For whole roots only 125 | bool showDistMap = false; 126 | bool showMedialAxis = true; 127 | int medialaxiswidth = 3; 128 | bool showMedialAxisDiameter = true; 129 | bool showContours = true; 130 | int contourwidth = 1; 131 | 132 | 133 | // Batch processing options 134 | bool batchmode = false; 135 | bool savesegmented = false; 136 | bool saveprocessed = false; 137 | QString segsuffix, prosuffix; 138 | QString featurecsvfile = "features.csv"; 139 | QString metadatacsvfile = "metadata.csv"; 140 | 141 | // Needed reporting progress in interactive mode. 142 | MainUI *ui; 143 | bool abortprocess = false; 144 | 145 | // Used for logging messages 146 | QString imagename; 147 | } feature_config; 148 | 149 | class CheckEnabler : public QWidget 150 | { 151 | Q_OBJECT; 152 | 153 | private: 154 | QCheckBox *cb; 155 | QLineEdit *edt; 156 | QLabel *lbl; 157 | 158 | QHBoxLayout *layout; 159 | std::vector widgets; 160 | 161 | public: 162 | CheckEnabler(QString text, QString lbl, bool integervalue = false, QWidget *parent = nullptr); 163 | 164 | bool checked() const { return cb->isChecked(); }; 165 | void setChecked(bool on) { cb->setChecked(on); }; 166 | double getValue() const { return edt->text().toDouble(); }; 167 | void setValue(double val) { edt->setText(QString::number(val, 'g')); }; 168 | void setValue(QString val) { edt->setText(val); }; 169 | void setLabelText(QString text) { lbl->setText(text); }; 170 | 171 | void addToLayout(QWidget *w) { layout->addWidget(w, 0, Qt::AlignLeft); widgets.push_back(w); this->update(); } 172 | //void setWhatsThis(const QString &msg) { QWidget::setWhatsThis(msg); } 173 | 174 | signals: 175 | void stateChanged(); 176 | void textChanged(); 177 | }; 178 | 179 | class StringCheckEnabler : public QWidget 180 | { 181 | Q_OBJECT; 182 | 183 | private: 184 | QCheckBox *cb; 185 | QLineEdit *edt; 186 | QLabel *lbl; 187 | 188 | public: 189 | StringCheckEnabler(QString text, QString lbl, QWidget *parent = nullptr); 190 | 191 | bool checked() const { return cb->isChecked(); }; 192 | void setChecked(bool on) { cb->setChecked(on); }; 193 | QString getValue() const { return edt->text(); }; 194 | void setValue(QString val) { edt->setText(val); }; 195 | 196 | //void setWhatsThis(const QString &msg) { QWidget::setWhatsThis(msg); } 197 | 198 | signals: 199 | void stateChanged(); 200 | void textChanged(); 201 | }; 202 | 203 | class MainUI : public QObject, public IPlugin 204 | { 205 | Q_OBJECT; 206 | Q_INTERFACES(IPlugin); 207 | Q_PLUGIN_METADATA(IID IPlugin_iid FILE "RhizoVisionExplorer.json"); 208 | 209 | public: 210 | typedef void(*processfunc)(feature_config* config); 211 | 212 | MainUI(); 213 | //~MainUI(); 214 | void setprocessfunction(processfunc pfunc); 215 | void setHostWindow(cvutil::cvutilWindow *wnd); 216 | 217 | //private: 218 | //MainUI(std::shared_ptr fconfig); 219 | public slots: 220 | std::string getName(); 221 | AppType getApplicationType(); 222 | OutputType getOutputType(); 223 | std::string getAlgorithmName(); 224 | std::vector getParameters(); 225 | QWidget *getPluginUI(); 226 | void setImage(cv::Mat image, QString imagename = ""); 227 | void execute(); 228 | std::vector getOutputImages(); 229 | int getDisplayIndex(); 230 | void setDisplayIndex(int idx); 231 | std::vector getFeatures(); 232 | std::vector getFeatures(int roiidx); 233 | void setBatchMode(bool on); 234 | int saveOutput(QString savloc, QString inputfilename); 235 | void saveMetadata(QString imgloc, QString savloc, QString filepath = ""); 236 | void loadMetadata(QString filepath); 237 | int writeHeader(QString savloc, QString filename = ""); 238 | std::vector getCSVColumnNames(); 239 | int getProgressSteps(); 240 | void abort(); 241 | QChart *getChart(); 242 | 243 | signals: 244 | void updateVisualOutput(cv::Mat m); 245 | void updateProgress(QString status); 246 | 247 | private: 248 | void createOptions(); 249 | void createRangeControls(); 250 | void updateRangeControls(); 251 | void enablepixelconversion(); 252 | void connectSignalstoSlots(); 253 | //void enableinvertimage(); 254 | //void enablesavesegmented(); 255 | //void enablesaveprocessed(); 256 | void updateconversion(); 257 | void setTextWhatsThis(); 258 | void spboxvaluechanged(QDoubleSpinBox *s, double k); 259 | void addrangerowclicked(double lastdrange = -1.0f); 260 | void removerangerowclicked(); 261 | void colorizechart(QChart *chart, int size); 262 | 263 | private slots: 264 | void updatesegmentedoutput(); 265 | 266 | private: 267 | QVBoxLayout *vlayout; 268 | QLabel *lbroottype, *lbdispoutput; 269 | QComboBox *roottype, *dispoutput, *pixelspermm; 270 | //QCheckBox *invertimage; //, *savesegmented, *saveprocessed; // , *convertunits; 271 | //QCheckBox *enableRootPruning; 272 | QPushButton *pbpreview; 273 | cv::Ptr
f; 274 | QIcon rightarrow, downarrow; 275 | 276 | bool dispoutputupdating = false; 277 | bool executing = false; // Gaurd to prevent thread unsafe way to update config->displayOutputIndex. 278 | std::vector drangeview; // To synchronize diameter range view (UI) and the internal list (config->drange). 279 | 280 | StringCheckEnabler *saveseg, *savepro; 281 | CheckEnabler *convertunits, *linesmooth, *filterbknoisy, *filterfgnoisy, *enableRootPruning; 282 | QLabel *ranges; 283 | QLineEdit *featurefileedt, *metadatafileedt; 284 | QCheckBox *keepLargest; 285 | 286 | std::vector dranges; 287 | std::vector editmins; 288 | std::vector spboxes; 289 | QPushButton *addrangerow, *removerangerow; 290 | 291 | QLabel* thresh; 292 | QSlider *thresholdslider; 293 | QSpinBox *thresholdbox; 294 | QProgressBar *thresholdbar; 295 | 296 | QCheckBox *showConvexHull, *showHoles; // For whole root only 297 | QCheckBox *showDistMap, *showMedialAxisDiameter; 298 | CheckEnabler *showMedialAxis, *showContours; 299 | 300 | //int roottypeval = 0; 301 | std::shared_ptr config; 302 | processfunc pfunc; 303 | 304 | cvutilWindow* hostWindow = nullptr; 305 | QScrollArea *pluginuiarea = nullptr; 306 | QToolBox *pluginui = nullptr; 307 | }; 308 | 309 | #endif // DIALOG_H 310 | 311 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/RhizoVisionExplorer.json: -------------------------------------------------------------------------------- 1 | { } -------------------------------------------------------------------------------- /RhizoVisionExplorer/RhizoVisionExplorer.rc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/predictivephenomics/RhizoVisionExplorer/42750c9d238153dd2d707267c70dcbe66e302083/RhizoVisionExplorer/RhizoVisionExplorer.rc -------------------------------------------------------------------------------- /RhizoVisionExplorer/RhizoVisionExplorer.vcxproj: 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"C:\Users\aseethepalli\Documents\projects\GITRepositories\cvutil\build\cvutil\bin\Qt5Core.dll" "$(TargetDir)" /Y 190 | xcopy "C:\Users\aseethepalli\Documents\projects\GITRepositories\cvutil\build\cvutil\bin\Qt5Gui.dll" "$(TargetDir)" /Y 191 | xcopy "C:\Users\aseethepalli\Documents\projects\GITRepositories\cvutil\build\cvutil\bin\Qt5Widgets.dll" "$(TargetDir)" /Y 192 | xcopy "C:\Users\aseethepalli\Documents\projects\GITRepositories\cvutil\build\RoiManager\bin\RoiManager.dll" "$(TargetDir)" /Y 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 | 205 | 206 | 207 | 208 | 209 | 210 | 211 | 212 | 213 | 214 | 215 | Designer 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/RhizoVisionExplorer.vcxproj.filters: -------------------------------------------------------------------------------- 1 |  2 | 3 | 4 | 5 | {4FC737F1-C7A5-4376-A066-2A32D752A2FF} 6 | cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx 7 | 8 | 9 | {93995380-89BD-4b04-88EB-625FBE52EBFB} 10 | h;hh;hpp;hxx;hm;inl;inc;xsd 11 | 12 | 13 | {67DA6AB6-F800-4c08-8B7A-83BB121AAD01} 14 | rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav;mfcribbon-ms 15 | 16 | 17 | 18 | 19 | Source Files 20 | 21 | 22 | Source Files 23 | 24 | 25 | Source Files 26 | 27 | 28 | Source Files 29 | 30 | 31 | Source Files 32 | 33 | 34 | Source Files 35 | 36 | 37 | 38 | 39 | Header Files 40 | 41 | 42 | Header Files 43 | 44 | 45 | Header Files 46 | 47 | 48 | Source Files 49 | 50 | 51 | Header Files 52 | 53 | 54 | Header Files 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | Resource Files 64 | 65 | 66 | 67 | 68 | Resource Files 69 | 70 | 71 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/RhizoVisionExplorer.vcxproj.user: -------------------------------------------------------------------------------- 1 |  2 | 3 | 4 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/common_types.h: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (C) 2021, Anand Seethepalli and Larry York 3 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 4 | 5 | File: common_types.h 6 | 7 | Authors: 8 | Anand Seethepalli (anand.seethepalli@yahoo.co.in) 9 | Larry York (larry.york@gmail.com) 10 | 11 | This file is part of RhizoVision Explorer. 12 | 13 | RhizoVision Explorer is free software: you can redistribute 14 | it and/or modify it under the terms of the GNU General Public 15 | License as published by the Free Software Foundation, either 16 | version 3 of the License, or (at your option) any later version. 17 | 18 | RhizoVision Explorer is distributed in the hope that it will 19 | be useful, but WITHOUT ANY WARRANTY; without even the implied 20 | warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 21 | PURPOSE. See the GNU General Public License for more details. 22 | 23 | You should have received a copy of the GNU General Public 24 | License along with RhizoVision Explorer; see the file COPYING. 25 | If not, see . 26 | */ 27 | 28 | #pragma once 29 | 30 | #ifndef COMMON_TYPES_H 31 | #define COMMON_TYPES_H 32 | 33 | #include 34 | 35 | using namespace cvutil; 36 | 37 | template 38 | using ListRef = std::vector&; 39 | 40 | typedef ListRef IndexList; 41 | typedef std::vector Indices; 42 | typedef ListRef ValueList; 43 | typedef std::vector Values; 44 | 45 | typedef ListRef PointList; 46 | typedef std::vector Points; 47 | 48 | template 49 | using ListofListsRef = std::vector>&; 50 | 51 | template 52 | using ListofLists = std::vector>; 53 | 54 | template 55 | using ListofListsPtr = std::vector>*; 56 | 57 | template 58 | using Dictionary = std::unordered_map; 59 | 60 | template 61 | using DictionaryRef = std::unordered_map&; 62 | 63 | #endif 64 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/demo.h: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (C) 2021, Anand Seethepalli and Larry York 3 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 4 | 5 | File: demo.h 6 | 7 | Authors: 8 | Anand Seethepalli (anand.seethepalli@yahoo.co.in) 9 | Larry York (larry.york@gmail.com) 10 | 11 | This file is part of RhizoVision Explorer. 12 | 13 | RhizoVision Explorer is free software: you can redistribute 14 | it and/or modify it under the terms of the GNU General Public 15 | License as published by the Free Software Foundation, either 16 | version 3 of the License, or (at your option) any later version. 17 | 18 | RhizoVision Explorer is distributed in the hope that it will 19 | be useful, but WITHOUT ANY WARRANTY; without even the implied 20 | warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 21 | PURPOSE. See the GNU General Public License for more details. 22 | 23 | You should have received a copy of the GNU General Public 24 | License along with RhizoVision Explorer; see the file COPYING. 25 | If not, see . 26 | */ 27 | 28 | #pragma once 29 | 30 | #ifndef DEMO_H 31 | #define DEMO_H 32 | 33 | #include "cvutil.h" 34 | 35 | #include 36 | 37 | std::vector> getholes(std::vector> cc, cv::Size sz) 38 | { 39 | std::vector> result; 40 | int outercomp = -1, nr, nc; 41 | result.resize(cc.size() - 1); 42 | 43 | for (int i = 0; i < cc.size(); i++) 44 | { 45 | for (int j = 0; j < cc[i].size(); j++) 46 | { 47 | nr = cc[i][j] / sz.width; 48 | nc = cc[i][j] % sz.width; 49 | 50 | if (nr == 0 || nc == 0 || 51 | nr == (sz.height - 1) || 52 | nc == (sz.width - 1)) 53 | { 54 | outercomp = i; 55 | break; 56 | } 57 | } 58 | } 59 | 60 | for (int i = 0, j = 0; i < cc.size(); i++) 61 | { 62 | if (i != outercomp) 63 | { 64 | result[j] = cc[i]; 65 | j++; 66 | } 67 | } 68 | 69 | return result; 70 | } 71 | 72 | std::vector getComponentCentroid(std::vector> cc, cv::Size sz) 73 | { 74 | unsigned long long rowsum, colsum; 75 | std::vector result; 76 | result.resize(cc.size()); 77 | 78 | for (int i = 0; i < cc.size(); i++) 79 | { 80 | rowsum = 0; 81 | colsum = 0; 82 | 83 | for (int j = 0; j < cc[i].size(); j++) 84 | { 85 | rowsum += (cc[i][j] / sz.width); 86 | colsum += (cc[i][j] % sz.width); 87 | } 88 | 89 | rowsum /= cc[i].size(); 90 | colsum /= cc[i].size(); 91 | result[i] = rowsum * sz.width + colsum; 92 | } 93 | 94 | return result; 95 | } 96 | 97 | cv::Mat pdist2(std::vector pts, cv::Size sz) 98 | { 99 | cv::Mat m = cv::Mat(pts); 100 | m.convertTo(m, CV_32FC1); 101 | cv::Mat mr, mc, repmr, repmc, sqrepmr, sqrepmc, result; 102 | 103 | mr = floor(m / sz.width); 104 | mc = m - floor(m / sz.width) * sz.width; 105 | 106 | repmr = repeat(mr, 1, mr.rows); 107 | sqrepmr = repmr.mul(repmr); 108 | 109 | repmc = repeat(mc, 1, mc.rows); 110 | sqrepmc = repmc.mul(repmc); 111 | 112 | result = sqrepmr + sqrepmr.t() + ((repmr.mul(repmr.t())) * (-2)); 113 | result = result + sqrepmc + sqrepmc.t() + ((repmc.mul(repmc.t())) * (-2)); 114 | 115 | return result; 116 | } 117 | 118 | cv::Mat getnearestcomponents(cv::Mat distmap) 119 | { 120 | cv::Mat result = cv::Mat::zeros(distmap.rows, 4, CV_32SC1); 121 | int *resultptr = result.ptr(); 122 | float *distptr = distmap.ptr(); 123 | std::vector val = { FLT_MAX, FLT_MAX, FLT_MAX, FLT_MAX }; 124 | std::vector pos = { -1, -1, -1, -1 }; 125 | 126 | for (int i = 0; i < distmap.rows; i++) 127 | { 128 | val = { FLT_MAX, FLT_MAX, FLT_MAX, FLT_MAX }; 129 | pos = { -1, -1, -1, -1 }; 130 | 131 | for (int j = i + 1; j < distmap.rows; j++) 132 | { 133 | if (distptr[j] < val[0]) 134 | { 135 | pos[3] = pos[2]; 136 | val[3] = val[2]; 137 | 138 | pos[2] = pos[1]; 139 | val[2] = val[1]; 140 | 141 | pos[1] = pos[0]; 142 | val[1] = val[0]; 143 | 144 | pos[0] = j; 145 | val[0] = distptr[j]; 146 | } 147 | else if (distptr[j] < val[1]) 148 | { 149 | pos[3] = pos[2]; 150 | val[3] = val[2]; 151 | 152 | pos[2] = pos[1]; 153 | val[2] = val[1]; 154 | 155 | pos[1] = j; 156 | val[1] = distptr[j]; 157 | } 158 | else if (distptr[j] < val[2]) 159 | { 160 | pos[3] = pos[2]; 161 | val[3] = val[2]; 162 | 163 | pos[2] = j; 164 | val[2] = distptr[j]; 165 | } 166 | else if (distptr[j] < val[3]) 167 | { 168 | pos[3] = j; 169 | val[3] = distptr[j]; 170 | } 171 | } 172 | 173 | resultptr[i * 4] = pos[0]; 174 | resultptr[i * 4 + 1] = pos[1]; 175 | resultptr[i * 4 + 2] = pos[2]; 176 | resultptr[i * 4 + 3] = pos[3]; 177 | } 178 | 179 | return result; 180 | } 181 | 182 | std::vector getcolorcodes(cv::Mat nearest) 183 | { 184 | std::vector result; 185 | int *nearestptr = nearest.ptr(); 186 | result.resize(nearest.rows); 187 | std::vector colors = { 1,2,3,4,5 }, cols, vcols; 188 | std::unordered_map cm; 189 | int found = 0; 190 | std::random_device rng; 191 | std::mt19937 urng(rng()); 192 | 193 | for (int i = 0; i < nearest.rows; i++) 194 | { 195 | if (i == 0) 196 | { 197 | result[i] = colors[0]; 198 | cm[i] = colors[0]; 199 | 200 | for (int j = 0; j < 4; j++) 201 | { 202 | result[nearestptr[i * 4 + j]] = colors[j + 1]; 203 | cm[nearestptr[i * 4 + j]] = colors[j + 1]; 204 | } 205 | 206 | continue; 207 | } 208 | 209 | cols.clear(); 210 | vcols.clear(); 211 | 212 | if (cm[i] != 0) 213 | cols.push_back(cm[i]); 214 | 215 | for (int j = 0; j < 4; j++) 216 | { 217 | if (nearestptr[i * 4 + j] != -1 && cm[nearestptr[i * 4 + j]] != 0) 218 | cols.push_back(cm[nearestptr[i * 4 + j]]); 219 | } 220 | 221 | for (int j = 0; j < colors.size(); j++) 222 | { 223 | found = 0; 224 | 225 | for (int k = 0; k < cols.size(); k++) 226 | { 227 | if (cols[k] == colors[j]) 228 | { 229 | found = 1; 230 | break; 231 | } 232 | } 233 | 234 | if (found == 0) 235 | vcols.push_back(colors[j]); 236 | } 237 | 238 | std::shuffle(vcols.begin(), vcols.end(), urng); 239 | 240 | if (cm[i] == 0) 241 | { 242 | result[i] = vcols[0]; 243 | cm[i] = vcols[0]; 244 | 245 | for (int j = 0, k = 1; j < 4; j++) 246 | { 247 | if (nearestptr[i * 4 + j] != -1 && cm[nearestptr[i * 4 + j]] == 0) 248 | { 249 | result[nearestptr[i * 4 + j]] = vcols[k]; 250 | cm[nearestptr[i * 4 + j]] = vcols[k]; 251 | k++; 252 | } 253 | } 254 | } 255 | else 256 | { 257 | for (int j = 0, k = 0; j < 4; j++) 258 | { 259 | if (nearestptr[i * 4 + j] != -1 && cm[nearestptr[i * 4 + j]] == 0) 260 | { 261 | result[nearestptr[i * 4 + j]] = vcols[k]; 262 | cm[nearestptr[i * 4 + j]] = vcols[k]; 263 | k++; 264 | } 265 | } 266 | } 267 | } 268 | 269 | return result; 270 | } 271 | 272 | #endif 273 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/icons/RVElogoclearback-150.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/predictivephenomics/RhizoVisionExplorer/42750c9d238153dd2d707267c70dcbe66e302083/RhizoVisionExplorer/icons/RVElogoclearback-150.png -------------------------------------------------------------------------------- /RhizoVisionExplorer/icons/RVElogoclearback.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/predictivephenomics/RhizoVisionExplorer/42750c9d238153dd2d707267c70dcbe66e302083/RhizoVisionExplorer/icons/RVElogoclearback.png -------------------------------------------------------------------------------- /RhizoVisionExplorer/icons/rveicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/predictivephenomics/RhizoVisionExplorer/42750c9d238153dd2d707267c70dcbe66e302083/RhizoVisionExplorer/icons/rveicon.ico -------------------------------------------------------------------------------- /RhizoVisionExplorer/main.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (C) 2021, Anand Seethepalli and Larry York 3 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 4 | 5 | File: main.cpp 6 | 7 | Authors: 8 | Anand Seethepalli (anand.seethepalli@yahoo.co.in) 9 | Larry York (larry.york@gmail.com) 10 | 11 | This file is part of RhizoVision Explorer. 12 | 13 | RhizoVision Explorer is free software: you can redistribute 14 | it and/or modify it under the terms of the GNU General Public 15 | License as published by the Free Software Foundation, either 16 | version 3 of the License, or (at your option) any later version. 17 | 18 | RhizoVision Explorer is distributed in the hope that it will 19 | be useful, but WITHOUT ANY WARRANTY; without even the implied 20 | warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 21 | PURPOSE. See the GNU General Public License for more details. 22 | 23 | You should have received a copy of the GNU General Public 24 | License along with RhizoVision Explorer; see the file COPYING. 25 | If not, see . 26 | */ 27 | 28 | #include 29 | 30 | #include 31 | #include 32 | 33 | #include "common_types.h" 34 | #include "roottopology.h" 35 | #include "rootsegmentprop.h" 36 | #include "demo.h" 37 | #include "MainUI.h" 38 | 39 | #include 40 | 41 | using namespace std; 42 | using namespace cv; 43 | using namespace cvutil; 44 | 45 | //#ifdef NDEBUG 46 | //#define DEBUG_MODE 47 | //#endif 48 | 49 | ///////////////// Program configuration data /////////////// 50 | const string saveloc = "C:/Users/aseethepalli/Documents/projects/hundredhours2/"; 51 | const string features_filename = "./pics/features.txt"; 52 | //const double pixel2mm = 127 / 2408.2; //1.0; // 76.0 / 784.2; 53 | const bool showprocessedimage = true; 54 | Ptr vseg, vpro; 55 | int rwidth1 = 400, rwidth2 = 400, cwidth1 = 800, cwidth2 = 800; 56 | //////////////////////////////////////////////////////////// 57 | 58 | void getMedianMaxRootNumbers(Mat seg, double &medrtno, double &maxrtno) 59 | { 60 | Mat seg1, seg2, diff, m, m2; 61 | double *mptr; 62 | int zidx = 0; 63 | 64 | hconcat(Mat::zeros(seg.rows, 1, seg.type()), seg, seg1); 65 | hconcat(seg, Mat::zeros(seg.rows, 1, seg.type()), seg2); 66 | diff = seg1 - seg2; 67 | 68 | diff = (diff > 0) / 255; 69 | reduce(diff, m, 1, CV_REDUCE_SUM, CV_MAKE_TYPE(CV_MAT_DEPTH(CV_64F), diff.channels())); 70 | 71 | std::sort(m.ptr(), m.ptr() + m.rows); 72 | //cv::sort(m, m2, cv::SortFlags::SORT_DESCENDING); 73 | mptr = m.ptr(); 74 | maxrtno = mptr[m.rows - 1]; 75 | 76 | for (; mptr[zidx] == 0; zidx++); 77 | 78 | medrtno = ((m.rows - zidx) % 2 == 0) ? ((mptr[(m.rows - zidx) / 2 + zidx] + mptr[(m.rows - zidx) / 2 - 1 + zidx]) / 2.0) 79 | : mptr[(m.rows - zidx) / 2 + zidx]; 80 | } 81 | 82 | double getperimeterlength(vector> &contours) 83 | { 84 | double perimeter = 0.0; 85 | Point diff; 86 | 87 | for (auto &c : contours) 88 | { 89 | for (int i = 0; i < (c.size() - 1); i++) 90 | { 91 | diff = c[i] - c[i + 1]; 92 | perimeter += sqrt(diff.ddot(diff)); 93 | } 94 | 95 | diff = c[0] - c[c.size() - 1]; 96 | perimeter += sqrt(diff.ddot(diff)); 97 | } 98 | 99 | return perimeter; 100 | } 101 | 102 | void getavgrootradius(ListofListsRef radii, double &medradius, double& avgradius) 103 | { 104 | int rsize = 0; 105 | avgradius = 0.0; 106 | medradius = 0.0; 107 | Values rd; 108 | 109 | if (radii.size() == 0) 110 | return; 111 | 112 | for (int i = 0; i < radii.size(); i++) 113 | rd.insert(rd.end(), radii[i].begin(), radii[i].end()); 114 | 115 | sort(rd.begin(), rd.end()); 116 | 117 | if ((rd.size() % 2) == 0) 118 | medradius = (rd[rd.size() / 2 - 1] + rd[rd.size() / 2]) / 2.0; 119 | else 120 | medradius = rd[rd.size() / 2 - 1]; 121 | 122 | for (int i = 0; i < radii.size(); i++) 123 | { 124 | for (int j = 0; j < radii[i].size(); j++) 125 | avgradius += radii[i][j]; 126 | 127 | rsize += static_cast(radii[i].size()); 128 | } 129 | 130 | avgradius /= double(rsize); 131 | } 132 | 133 | void getvolumesurfacearea(Mat skeleton, Mat dist, ListofListsRef segments, PointList overlap, double& volume, double& surfacearea) 134 | { 135 | int i, j, x, y, xinc, yinc, currx, curry, nextx, nexty, nnextpt, fxinc, fyinc; 136 | double rad = 0, sqr = sqrt(2), dv = 0, dvol = 0, dsa = 0; 137 | size_t cisz; 138 | 139 | float *dtptr = dist.ptr(); 140 | uchar *skel = skeleton.ptr(); 141 | 142 | volume = 0.0; 143 | surfacearea = 0.0; 144 | 145 | for (i = 0; i < segments.size(); i++) 146 | { 147 | cisz = segments[i].size() - 1; 148 | 149 | for (j = 0; j < cisz; j++) 150 | { 151 | nnextpt = j + 1; 152 | 153 | currx = segments[i][j].x; 154 | curry = segments[i][j].y; 155 | nextx = segments[i][nnextpt].x; 156 | nexty = segments[i][nnextpt].y; 157 | 158 | if (nextx != currx) 159 | xinc = abs(currx - nextx) / (nextx - currx); 160 | else 161 | xinc = 0; 162 | 163 | if (nexty != curry) 164 | yinc = abs(curry - nexty) / (nexty - curry); 165 | else 166 | yinc = 0; 167 | 168 | fxinc = fabs(xinc); 169 | fyinc = fabs(yinc); 170 | rad = fxinc + fyinc; 171 | rad = (rad == 2.0) ? CVUTIL_SQRT2 : rad; 172 | 173 | for (x = currx, y = curry; !(x == nextx && y == nexty); x += xinc, y += yinc) 174 | { 175 | dv = dtptr[y * dist.cols + x]; 176 | dvol += (CV_PI * dv * dv * rad); 177 | dsa += (2.0 * CV_PI * dv * rad); 178 | } 179 | } 180 | 181 | /*dv = dtptr[y * dist.cols + x]; 182 | dvol += (CV_PI * dv * dv); 183 | dsa += (2.0 * CV_PI * dv);*/ 184 | } 185 | 186 | for (auto &overlappt : overlap) 187 | { 188 | // To check if the overlappt is a diagonal or orthogonal 189 | if (skel[overlappt.y * skeleton.cols + overlappt.x + 1] > 0) 190 | { 191 | // Orthogonal 192 | dv = dtptr[overlappt.y * dist.cols + overlappt.x]; 193 | dvol += (CV_PI * dv * dv); 194 | dsa += (2.0 * CV_PI * dv); 195 | } 196 | else 197 | { 198 | // Diagonal 199 | dv = dtptr[overlappt.y * dist.cols + overlappt.x]; 200 | dvol += (CV_PI * dv * dv * CVUTIL_SQRT2); 201 | dsa += (2.0 * CV_PI * dv * CVUTIL_SQRT2); 202 | } 203 | } 204 | 205 | volume = dvol; 206 | surfacearea = dsa; 207 | } 208 | 209 | void getdiameterrangehistograms(Mat skeleton, Mat dist, ListofListsRef segments, PointList overlap, Values rranges, 210 | ValueList rootlengthhist, ValueList projareahist, ValueList sahist, ValueList vhist, double &rootlength, double &volume, double &sarea) 211 | /*double& coarse, double& medium, double& fine*///double dlo, double dhi) 212 | { 213 | int i, j, k, x, y, xinc, yinc, currx, curry, nextx, nexty, nnextpt, fxinc, fyinc, didx; 214 | double rad = 0, sqr = sqrt(2.0), dv = 0; 215 | size_t cisz; 216 | 217 | size_t rsize = rranges.size(); 218 | rootlengthhist.resize(rsize + 1); 219 | projareahist.resize(rsize + 1); 220 | sahist.resize(rsize + 1); 221 | vhist.resize(rsize + 1); 222 | 223 | Mat radrange = Mat::zeros(dist.size(), CV_8UC1); 224 | 225 | if (rsize > 0) 226 | { 227 | for (k = 0; k < (rsize - 1); k++) 228 | { 229 | rootlengthhist[k] = 0.0; 230 | projareahist[k] = 0.0; 231 | sahist[k] = 0.0; 232 | vhist[k] = 0.0; 233 | 234 | radrange = radrange + (((dist <= rranges[k + 1]) - (dist <= rranges[k])) / 255u) * uint8_t(k + 1); 235 | } 236 | 237 | rootlengthhist[rsize - 1] = 0.0; 238 | projareahist[rsize - 1] = 0.0; 239 | sahist[rsize - 1] = 0.0; 240 | vhist[rsize - 1] = 0.0; 241 | 242 | radrange = radrange + ((dist > rranges[rsize - 1]) / 255u) * uint8_t(rsize); 243 | } 244 | else 245 | { 246 | rootlengthhist[0] = 0.0; 247 | projareahist[0] = 0.0; 248 | sahist[0] = 0.0; 249 | vhist[0] = 0.0; 250 | } 251 | 252 | float *dtptr = dist.ptr(); 253 | uchar *skel = skeleton.ptr(); 254 | uchar *rptr = radrange.ptr(); 255 | 256 | for (i = 0; i < segments.size(); i++) 257 | { 258 | cisz = segments[i].size() - 1; 259 | 260 | for (j = 0; j < cisz; j++) 261 | { 262 | nnextpt = j + 1; 263 | 264 | currx = segments[i][j].x; 265 | curry = segments[i][j].y; 266 | nextx = segments[i][nnextpt].x; 267 | nexty = segments[i][nnextpt].y; 268 | 269 | if (nextx != currx) 270 | xinc = abs(currx - nextx) / (nextx - currx); 271 | else 272 | xinc = 0; 273 | 274 | if (nexty != curry) 275 | yinc = abs(curry - nexty) / (nexty - curry); 276 | else 277 | yinc = 0; 278 | 279 | fxinc = fabs(xinc); 280 | fyinc = fabs(yinc); 281 | rad = fxinc + fyinc; 282 | rad = (rad == 2.0) ? CVUTIL_SQRT2 : rad; 283 | 284 | for (x = currx, y = curry; !(x == nextx && y == nexty); x += xinc, y += yinc) 285 | { 286 | dv = dtptr[y * dist.cols + x]; 287 | didx = rptr[y * dist.cols + x]; 288 | 289 | rootlengthhist[didx] += rad; 290 | projareahist[didx] += (2 * dv * rad); 291 | vhist[didx] += (CV_PI * dv * dv * rad); 292 | sahist[didx] += (2.0 * CV_PI * dv * rad); 293 | } 294 | } 295 | 296 | /*dv = dtptr[y * dist.cols + x]; 297 | didx = rptr[y * dist.cols + x]; 298 | 299 | rootlengthhist[didx] += rad; 300 | projareahist[didx] += (2 * dv * rad); 301 | vhist[didx] += (CV_PI * dv * dv * rad); 302 | sahist[didx] += (2.0 * CV_PI * dv * rad); 303 | */ 304 | } 305 | 306 | for (auto &overlappt : overlap) 307 | { 308 | // To check if the overlappt is a diagonal or orthogonal 309 | if (skel[overlappt.y * skeleton.cols + overlappt.x + 1] > 0) 310 | { 311 | // Orthogonal 312 | dv = dtptr[overlappt.y * dist.cols + overlappt.x]; 313 | didx = rptr[overlappt.y * dist.cols + overlappt.x]; 314 | 315 | rootlengthhist[didx] += 1.0; 316 | //projareahist[didx] += (2 * dv * rad); 317 | vhist[didx] += (CV_PI * dv * dv); 318 | sahist[didx] += (2.0 * CV_PI * dv); 319 | } 320 | else 321 | { 322 | // Diagonal 323 | dv = dtptr[overlappt.y * dist.cols + overlappt.x]; 324 | didx = rptr[overlappt.y * dist.cols + overlappt.x]; 325 | 326 | rootlengthhist[didx] += CVUTIL_SQRT2; 327 | //projareahist[didx] += (2 * dv * rad); 328 | vhist[didx] += (CV_PI * dv * dv * CVUTIL_SQRT2); 329 | sahist[didx] += (2.0 * CV_PI * dv * CVUTIL_SQRT2); 330 | } 331 | } 332 | 333 | // Now to add the histograms to get total root length, volume 334 | // and surface area. 335 | rootlength = 0; 336 | volume = 0; 337 | sarea = 0; 338 | for (i = 0; i < rootlengthhist.size(); i++) 339 | { 340 | rootlength += rootlengthhist[i]; 341 | volume += vhist[i]; 342 | sarea += sahist[i]; 343 | } 344 | } 345 | 346 | void getdiameterrangehistograms(Mat skeleton, Mat dist, ListofListsRef segments, PointList overlap, Values rranges, 347 | ValueList rootlengthhist, ValueList projareahist, ValueList sahist, ValueList vhist, double &rootlength, double &volume, double &sarea, Mat& rtdpoints) 348 | /*double& coarse, double& medium, double& fine*///double dlo, double dhi) 349 | { 350 | int i, j, k, x, y, xinc, yinc, currx, curry, nextx, nexty, nnextpt, fxinc, fyinc, didx; 351 | double rad = 0, sqr = sqrt(2.0), dv = 0; 352 | size_t cisz; 353 | map rdpoints; 354 | 355 | size_t rsize = rranges.size(); 356 | rootlengthhist.resize(rsize + 1); 357 | projareahist.resize(rsize + 1); 358 | sahist.resize(rsize + 1); 359 | vhist.resize(rsize + 1); 360 | 361 | Mat radrange = Mat::zeros(dist.size(), CV_8UC1); 362 | 363 | if (rsize > 0) 364 | { 365 | for (k = 0; k < (rsize - 1); k++) 366 | { 367 | rootlengthhist[k] = 0.0; 368 | projareahist[k] = 0.0; 369 | sahist[k] = 0.0; 370 | vhist[k] = 0.0; 371 | 372 | radrange = radrange + (((dist <= rranges[k + 1]) - (dist <= rranges[k])) / 255u) * uint8_t(k + 1); 373 | } 374 | 375 | rootlengthhist[rsize - 1] = 0.0; 376 | projareahist[rsize - 1] = 0.0; 377 | sahist[rsize - 1] = 0.0; 378 | vhist[rsize - 1] = 0.0; 379 | 380 | radrange = radrange + ((dist > rranges[rsize - 1]) / 255u) * uint8_t(rsize); 381 | } 382 | else 383 | { 384 | rootlengthhist[0] = 0.0; 385 | projareahist[0] = 0.0; 386 | sahist[0] = 0.0; 387 | vhist[0] = 0.0; 388 | } 389 | 390 | float *dtptr = dist.ptr(); 391 | uchar *skel = skeleton.ptr(); 392 | uchar *rptr = radrange.ptr(); 393 | 394 | for (i = 0; i < segments.size(); i++) 395 | { 396 | cisz = segments[i].size() - 1; 397 | 398 | for (j = 0; j < cisz; j++) 399 | { 400 | nnextpt = j + 1; 401 | 402 | currx = segments[i][j].x; 403 | curry = segments[i][j].y; 404 | nextx = segments[i][nnextpt].x; 405 | nexty = segments[i][nnextpt].y; 406 | 407 | if (nextx != currx) 408 | xinc = abs(currx - nextx) / (nextx - currx); 409 | else 410 | xinc = 0; 411 | 412 | if (nexty != curry) 413 | yinc = abs(curry - nexty) / (nexty - curry); 414 | else 415 | yinc = 0; 416 | 417 | fxinc = fabs(xinc); 418 | fyinc = fabs(yinc); 419 | rad = fxinc + fyinc; 420 | rad = (rad == 2.0) ? CVUTIL_SQRT2 : rad; 421 | 422 | for (x = currx, y = curry; !(x == nextx && y == nexty); x += xinc, y += yinc) 423 | { 424 | dv = dtptr[y * dist.cols + x]; 425 | didx = rptr[y * dist.cols + x]; 426 | 427 | rdpoints[dv] += rad; 428 | 429 | rootlengthhist[didx] += rad; 430 | projareahist[didx] += (2 * dv * rad); 431 | vhist[didx] += (CV_PI * dv * dv * rad); 432 | sahist[didx] += (2.0 * CV_PI * dv * rad); 433 | } 434 | } 435 | 436 | /*dv = dtptr[y * dist.cols + x]; 437 | didx = rptr[y * dist.cols + x]; 438 | 439 | rootlengthhist[didx] += rad; 440 | projareahist[didx] += (2 * dv * rad); 441 | vhist[didx] += (CV_PI * dv * dv * rad); 442 | sahist[didx] += (2.0 * CV_PI * dv * rad); 443 | */ 444 | } 445 | 446 | for (auto &overlappt : overlap) 447 | { 448 | // To check if the overlappt is a diagonal or orthogonal 449 | if (skel[overlappt.y * skeleton.cols + overlappt.x + 1] > 0) 450 | { 451 | // Orthogonal 452 | dv = dtptr[overlappt.y * dist.cols + overlappt.x]; 453 | didx = rptr[overlappt.y * dist.cols + overlappt.x]; 454 | 455 | rdpoints[dv] += 1.0; 456 | 457 | rootlengthhist[didx] += 1.0; 458 | //projareahist[didx] += (2 * dv * rad); 459 | vhist[didx] += (CV_PI * dv * dv); 460 | sahist[didx] += (2.0 * CV_PI * dv); 461 | } 462 | else 463 | { 464 | // Diagonal 465 | dv = dtptr[overlappt.y * dist.cols + overlappt.x]; 466 | didx = rptr[overlappt.y * dist.cols + overlappt.x]; 467 | 468 | rdpoints[dv] += CVUTIL_SQRT2; 469 | 470 | rootlengthhist[didx] += CVUTIL_SQRT2; 471 | //projareahist[didx] += (2 * dv * rad); 472 | vhist[didx] += (CV_PI * dv * dv * CVUTIL_SQRT2); 473 | sahist[didx] += (2.0 * CV_PI * dv * CVUTIL_SQRT2); 474 | } 475 | } 476 | 477 | rtdpoints = Mat::zeros(static_cast(rdpoints.size()), 2, CV_64FC1); 478 | double *rtdptr = rtdpoints.ptr(); 479 | 480 | int rtdidx = 0; 481 | for (auto& kv : rdpoints) 482 | { 483 | rtdptr[2 * rtdidx] = kv.first; 484 | rtdptr[2 * rtdidx + 1] = kv.second; 485 | 486 | rtdidx++; 487 | } 488 | 489 | // Now to add the histograms to get total root length, volume 490 | // and surface area. 491 | rootlength = 0; 492 | volume = 0; 493 | sarea = 0; 494 | for (i = 0; i < rootlengthhist.size(); i++) 495 | { 496 | rootlength += rootlengthhist[i]; 497 | volume += vhist[i]; 498 | sarea += sahist[i]; 499 | } 500 | } 501 | 502 | void getshallowdeeproots(ListofListsRef segments, double& shallow, double& medium, double& deep, double &avgangle) 503 | { 504 | shallow = 0.0; 505 | medium = 0.0; 506 | deep = 0.0; 507 | avgangle = 0.0; 508 | 509 | Mat m, m2, cov, me, lam, ev; 510 | double *evptr = nullptr; 511 | int i, j, k, x, y, nnextpt, currx, curry, nextx, nexty, xinc, yinc; 512 | size_t csz = segments.size(), cisz = 0, szcount = 0; 513 | int wsize = 20, nsamples = 0, npoints = 0, minv = 0, maxv = 0; 514 | double angle = 0; 515 | 516 | m.create(10000, 2, CV_64FC1); 517 | m2.create(wsize * wsize * 4, 2, CV_64FC1); 518 | 519 | double *mptr = m.ptr(), *mptr2 = m2.ptr(); 520 | 521 | for (i = 0, szcount = 0; i < csz; i++) 522 | { 523 | if (segments[i].size() <= 1) 524 | continue; 525 | 526 | // To reconstruct the full segment before getting 527 | // angle stats. 528 | cisz = segments[i].size() - 1; 529 | //szcount += cisz; 530 | 531 | //cout << "szcount = " << szcount << endl; 532 | 533 | for (j = 0, nsamples = 0; j < cisz; j++) 534 | { 535 | nnextpt = (j + 1); 536 | currx = segments[i][j].x; 537 | curry = segments[i][j].y; 538 | nextx = segments[i][nnextpt].x; 539 | nexty = segments[i][nnextpt].y; 540 | xinc = (currx == nextx) ? 0 : abs(currx - nextx) / (nextx - currx); 541 | yinc = (curry == nexty) ? 0 : abs(curry - nexty) / (nexty - curry); 542 | 543 | for (x = currx, y = curry; !(x == nextx && y == nexty); x += xinc, y += yinc) 544 | { 545 | mptr[nsamples * 2] = x; 546 | mptr[nsamples * 2 + 1] = y; 547 | nsamples++; 548 | } 549 | } 550 | 551 | mptr[nsamples * 2] = nextx; 552 | mptr[nsamples * 2 + 1] = nexty; 553 | nsamples++; 554 | 555 | // Now to browse through the segment using a 556 | // (2 * wsize + 1)-by-(2 * wsize + 1) window 557 | // and recording the orientation using the 558 | // eigen vectors from the covariance matix. 559 | for (j = 0; j < nsamples; j++) 560 | { 561 | npoints = 0; 562 | 563 | for (k = j; 564 | k < nsamples && 565 | abs(mptr[j * 2] - mptr[k * 2]) <= wsize && 566 | abs(mptr[j * 2 + 1] - mptr[k * 2 + 1]) <= wsize; 567 | k++) 568 | { 569 | mptr2[npoints * 2] = mptr[k * 2]; 570 | mptr2[npoints * 2 + 1] = mptr[k * 2 + 1]; 571 | npoints++; 572 | } 573 | 574 | for (k = (j - 1); 575 | k >= 0 && 576 | abs(mptr[j * 2] - mptr[k * 2]) <= wsize && 577 | abs(mptr[j * 2 + 1] - mptr[k * 2 + 1]) <= wsize; 578 | k--) 579 | { 580 | mptr2[npoints * 2] = mptr[k * 2]; 581 | mptr2[npoints * 2 + 1] = mptr[k * 2 + 1]; 582 | npoints++; 583 | } 584 | 585 | if (npoints > 1) 586 | { 587 | calcCovarMatrix(m2.rowRange(0, npoints), cov, me, COVAR_ROWS | COVAR_NORMAL); 588 | eigen(cov, lam, ev); 589 | evptr = ev.ptr(); 590 | angle = abs((atan(evptr[1] / evptr[0]) * 180.0) / CV_PI); 591 | 592 | avgangle = ((szcount * avgangle) + angle) / (szcount + 1); 593 | szcount++; 594 | 595 | if (angle <= 30) //(CV_PI / 6)) 596 | shallow++; 597 | else if (angle <= 60) //(CV_PI / 3)) 598 | medium++; 599 | else 600 | deep++; 601 | } 602 | } 603 | } 604 | 605 | angle = deep + medium + shallow; 606 | shallow /= angle; 607 | medium /= angle; 608 | deep /= angle; 609 | //avgangle /= szcount; 610 | 611 | m.release(); 612 | m2.release(); 613 | } 614 | 615 | void getshallowdeeprootsth(ListofListsRef segments, double& shallow, double& medium, double& deep, double &avgangle) 616 | { 617 | shallow = 0.0; 618 | medium = 0.0; 619 | deep = 0.0; 620 | avgangle = 0.0; 621 | 622 | int nthreads = getNumberOfCPUs() - 3; 623 | vector t(nthreads); 624 | vector tshallow(nthreads), tdeep(nthreads), tmedium(nthreads), tavgangle(nthreads), tcount(nthreads); 625 | vector m(nthreads), m2(nthreads); 626 | double anglev = 0, ncount = 0; 627 | 628 | for (int th = 0; th < nthreads; th++) 629 | { 630 | t[th] = thread([&](int thr) 631 | { 632 | int npoints = 0; 633 | Mat cov, me, lam, ev; 634 | double *evptr = nullptr; 635 | int i, j, k, x, y, nnextpt, currx, curry, nextx, nexty, xinc, yinc; 636 | size_t csz = segments.size(), cisz = 0, szcount = 0; 637 | int wsize = 20, nsamples = 0, minv = 0, maxv = 0; 638 | double angle = 0; 639 | 640 | m[thr].create(10000, 2, CV_64FC1); 641 | m2[thr].create(wsize * wsize * 4, 2, CV_64FC1); 642 | 643 | double *mptr = m[thr].ptr(), *mptr2 = m2[thr].ptr(); 644 | 645 | for (i = 0; i < csz; i++) 646 | { 647 | if (segments[i].size() <= 1) 648 | continue; 649 | 650 | // To reconstruct the full segment before getting 651 | // angle stats. 652 | cisz = segments[i].size() - 1; 653 | szcount += cisz; 654 | 655 | //cout << "szcount = " << szcount << endl; 656 | 657 | for (j = 0, nsamples = 0; j < cisz; j++) 658 | { 659 | nnextpt = (j + 1); 660 | currx = segments[i][j].x; 661 | curry = segments[i][j].y; 662 | nextx = segments[i][nnextpt].x; 663 | nexty = segments[i][nnextpt].y; 664 | xinc = (currx == nextx) ? 0 : abs(currx - nextx) / (nextx - currx); 665 | yinc = (curry == nexty) ? 0 : abs(curry - nexty) / (nexty - curry); 666 | 667 | for (x = currx, y = curry; (x != nextx && y != nexty); x += xinc, y += yinc) 668 | { 669 | mptr[nsamples * 2] = x; 670 | mptr[nsamples * 2 + 1] = y; 671 | nsamples++; 672 | } 673 | } 674 | 675 | mptr[nsamples * 2] = nextx; 676 | mptr[nsamples * 2 + 1] = nexty; 677 | nsamples++; 678 | 679 | // Now to browse through the segment using a 680 | // (2 * wsize + 1)-by-(2 * wsize + 1) window 681 | // and recording the orientation using the 682 | // eigen vectors from the covariance matix. 683 | for (j = 0; j < nsamples; j++) 684 | { 685 | npoints = 0; 686 | 687 | for (k = j; 688 | k < nsamples && 689 | abs(mptr[j * 2] - mptr[k * 2]) <= wsize && 690 | abs(mptr[j * 2 + 1] - mptr[k * 2 + 1]) <= wsize; 691 | k++) 692 | { 693 | mptr2[npoints * 2] = mptr[k * 2]; 694 | mptr2[npoints * 2 + 1] = mptr[k * 2 + 1]; 695 | npoints++; 696 | } 697 | 698 | for (k = (j - 1); 699 | k >= 0 && 700 | abs(mptr[j * 2] - mptr[k * 2]) <= wsize && 701 | abs(mptr[j * 2 + 1] - mptr[k * 2 + 1]) <= wsize; 702 | k--) 703 | { 704 | mptr2[npoints * 2] = mptr[k * 2]; 705 | mptr2[npoints * 2 + 1] = mptr[k * 2 + 1]; 706 | npoints++; 707 | } 708 | 709 | if (npoints > 1) 710 | { 711 | calcCovarMatrix(m2[thr].rowRange(0, npoints), cov, me, COVAR_ROWS); 712 | eigen(cov, lam, ev); 713 | evptr = ev.ptr(); 714 | angle = abs((atan(evptr[1] / evptr[0]) * 180.0) / CV_PI); 715 | tavgangle[thr] += angle; 716 | 717 | if (angle <= 30) //(CV_PI / 6)) 718 | tshallow[thr]++; 719 | else if (angle <= 60) //(CV_PI / 3)) 720 | tmedium[thr]++; 721 | else 722 | tdeep[thr]++; 723 | } 724 | } 725 | } 726 | 727 | m[thr].release(); 728 | m2[thr].release(); 729 | 730 | tcount[thr] = szcount; 731 | }, th); 732 | } 733 | 734 | for (int th = 0; th < nthreads; th++) 735 | { 736 | t[th].join(); 737 | 738 | deep += tdeep[th]; 739 | medium += tmedium[th]; 740 | shallow += tshallow[th]; 741 | 742 | ncount += tcount[th]; 743 | avgangle += tavgangle[th]; 744 | } 745 | 746 | anglev = deep + medium + shallow; 747 | shallow /= anglev; 748 | medium /= anglev; 749 | deep /= anglev; 750 | avgangle /= ncount; 751 | } 752 | 753 | bool checkProgress(feature_config* config, QString str) 754 | { 755 | config->ui->updateProgress(str); 756 | QApplication::processEvents(); 757 | return config->abortprocess; 758 | } 759 | 760 | //void feature_extractor(string filename, string savefolder, vector& featurevals, bool invertimage, bool saveseg, bool saveimages, bool pixelconv, double conversion, double rootlo, double roothi) 761 | void feature_extractor(feature_config* config) 762 | { 763 | Mat img, out, seg, lsim, lsimcropped, skel, dilatedskel, dist; 764 | Mat perimeter, hull, fhull, chull, dilatedhull, selement, merged, holes, pmap, nearest; 765 | vector> contours; 766 | vector> holepts; 767 | vector channels, hch; 768 | vector> hullpt; 769 | vector hierarchy; 770 | vector centroids, colorcodes; 771 | Points branchpts, endpts, overlappts; 772 | ListofLists rootsegments; 773 | ListofLists radii; 774 | double rootlength = -1.0, mediannoroots = -1.0, maxnoroots = -1.0; 775 | double perimeterlength = -1.0, medradius = -1.0, avgradius = -1.0, maxradius = -1.0; 776 | //double coarser = 0.0, mediumr = 0.0, finer = 0.0; 777 | Values rootlengthhist = {}, projareahist = {}, sahist = {}, vhist = {}; 778 | double shallowo = 0.0, mediumo = 0.0, deepo = 0.0, avgang = 0.0; 779 | double volume = -1.0, surfacearea = -1.0, vtime; 780 | int maxradrowidx = -1, nholes = 0; 781 | double pixel2mm = 1.0, avgholesize = 0.0; 782 | bool isborder = false, isborderholefound = false; 783 | //double diameterlo = config->rootlo, diameterhi = config->roothi; 784 | vector radiusranges; 785 | double nwarea = 0, convarea = 0, widthtodepthratio = 0, lowerrootarea = 0; 786 | std::random_device rng; 787 | std::mt19937 urng(rng()); 788 | int nfeatures; 789 | Mat rtdpoints; 790 | RotateFlags flag = ROTATE_90_CLOCKWISE, revflag = ROTATE_90_COUNTERCLOCKWISE; 791 | 792 | switch (config->rotation) 793 | { 794 | case 90: 795 | flag = ROTATE_90_CLOCKWISE; 796 | revflag = ROTATE_90_COUNTERCLOCKWISE; 797 | break; 798 | case 180: 799 | flag = ROTATE_180; 800 | revflag = ROTATE_180; 801 | break; 802 | case 270: 803 | flag = ROTATE_90_COUNTERCLOCKWISE; 804 | revflag = ROTATE_90_CLOCKWISE; 805 | break; 806 | } 807 | 808 | // Determine the number of features to be extracted 809 | if (config->roottype == 0) // crown root 810 | nfeatures = 24 + 4 * (static_cast(config->dranges.size()) + 1); 811 | else 812 | nfeatures = 12 + 4 * (static_cast(config->dranges.size()) + 1); 813 | 814 | #ifndef _DEBUG 815 | thread *t1; 816 | #endif 817 | 818 | vector> cc, colors = 819 | { { 228, 26, 28 }, 820 | { 55, 126, 184 }, 821 | { 77, 175, 74 }, 822 | { 152, 78, 163 }, 823 | { 255, 127, 0 } }; 824 | 825 | if (config->pixelconv) 826 | { 827 | if (config->pixelspermm == 0) // For DPI conversion 828 | pixel2mm /= (config->conversion / 25.4); 829 | else 830 | pixel2mm /= config->conversion; 831 | //diameterlo *= config->conversion; 832 | //diameterhi *= config->conversion; 833 | } 834 | 835 | // If the diameter ranges are given in mm, we need 836 | // to convert it to pixel units. 837 | for (auto &d : config->dranges) 838 | { 839 | if (!config->pixelconv) 840 | radiusranges.push_back(d / 2.0); 841 | else 842 | radiusranges.push_back(d / 2.0 / pixel2mm); 843 | } 844 | 845 | if (config->rotation != 0) 846 | rotate(config->input, img, flag); 847 | else 848 | img = config->input.clone(); 849 | 850 | if ((!config->batchmode) && checkProgress(config, "Thresholding the input image ...")) 851 | return; 852 | 853 | for (int ii = 0; ii < nfeatures; ii++) 854 | config->features.push_back(NAN); 855 | 856 | if (img.empty()) 857 | { 858 | //for (int ii = 0; ii < nfeatures; ii++) 859 | // config->features.push_back(NAN); 860 | 861 | Mat m1 = Mat::zeros(out.size(), out.type()); 862 | Mat m2 = Mat::ones(out.size(), out.type()) * 255u; 863 | if (!config->invertimage) 864 | m1 = (m1 < 128); 865 | 866 | if (config->rotation != 0) 867 | { 868 | rotate(m1, config->input, revflag); 869 | rotate(m2, config->processed, revflag); 870 | } 871 | else 872 | { 873 | config->seg = m1; 874 | config->processed = m2; 875 | } 876 | 877 | return; 878 | } 879 | 880 | srand(time(0)); 881 | tic(); 882 | 883 | if (config->invertimage) 884 | img = Scalar::all(255) - img; 885 | 886 | out = getSingleChannel(img < config->threshold, CV_8UC1); 887 | 888 | /*if (countNonZero(out) == 0) 889 | { 890 | Mat m1 = Mat::zeros(out.size(), out.type()); 891 | Mat m2 = Mat::ones(out.size(), out.type()) * 255u; 892 | if (!config->invertimage) 893 | m1 = (m1 < 128); 894 | 895 | if (config->rotation != 0) 896 | { 897 | rotate(m1, config->input, revflag); 898 | rotate(m2, config->processed, revflag); 899 | } 900 | else 901 | { 902 | config->seg = m1; 903 | config->processed = m2; 904 | } 905 | 906 | return; 907 | }*/ 908 | 909 | if ((!config->batchmode) && checkProgress(config, "Filtering noise ...")) 910 | return; 911 | 912 | if (config->roottype == 0 && config->keepLargest == true) 913 | seg = getLargestConnectedComponent(out); 914 | else 915 | { 916 | if ((!config->filterbknoise) && (!config->filterfgnoise)) 917 | seg = out.clone(); 918 | else 919 | { 920 | if (config->filterbknoise) 921 | seg = getImageFromComponents(out.size(), getConnectedComponents(out, (config->maxcompsizebk / pixel2mm) / pixel2mm)); 922 | if (config->filterfgnoise) 923 | seg = 255 - getImageFromComponents(seg.size(), getConnectedComponents(255 - seg, (config->maxcompsizefg / pixel2mm) / pixel2mm)); 924 | } 925 | } 926 | 927 | if (countNonZero(seg) == 0) 928 | { 929 | Mat m1 = Mat::zeros(out.size(), out.type()); 930 | Mat m2 = Mat::ones(out.size(), out.type()) * 255u; 931 | if (!config->invertimage) 932 | m1 = (m1 < 128); 933 | 934 | if (config->rotation != 0) 935 | { 936 | rotate(m1, config->input, revflag); 937 | rotate(m2, config->processed, revflag); 938 | } 939 | else 940 | { 941 | config->seg = m1; 942 | config->processed = m2; 943 | } 944 | 945 | return; 946 | } 947 | 948 | out = Mat(); 949 | 950 | Mat segcropped; 951 | auto fresultseg = find(seg>0, FindType::Subscripts); 952 | double rminseg = seg.rows, rmaxseg = -1, cminseg = seg.cols, cmaxseg = -1; 953 | int *rcpseg = fresultseg.first.ptr(); 954 | 955 | #ifndef _DEBUG 956 | for (int ii = 0; ii < fresultseg.first.rows; ii++) 957 | { 958 | if (rminseg > rcpseg[2 * ii]) 959 | rminseg = rcpseg[2 * ii]; 960 | if (cminseg > rcpseg[2 * ii + 1]) 961 | cminseg = rcpseg[2 * ii + 1]; 962 | if (rmaxseg < rcpseg[2 * ii]) 963 | rmaxseg = rcpseg[2 * ii]; 964 | if (cmaxseg < rcpseg[2 * ii + 1]) 965 | cmaxseg = rcpseg[2 * ii + 1]; 966 | } 967 | 968 | if ((rmaxseg + 2) <= seg.rows) 969 | rmaxseg += 2; 970 | else 971 | rmaxseg++; 972 | 973 | if ((cmaxseg + 2) <= seg.cols) 974 | cmaxseg += 2; 975 | else 976 | cmaxseg++; 977 | 978 | if ((cminseg - 1) >= 0) 979 | cminseg --; 980 | #else 981 | rminseg = 0; 982 | rmaxseg = seg.rows; 983 | cminseg = 0; 984 | cmaxseg = seg.cols; 985 | #endif 986 | 987 | if ((rmaxseg - rminseg) == 1 || (cmaxseg - cminseg) == 1) 988 | { 989 | return; 990 | } 991 | 992 | if (rmaxseg > rminseg || cmaxseg > cminseg) 993 | segcropped = seg.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg).clone(); 994 | else 995 | segcropped = seg.clone(); 996 | 997 | if ((!config->batchmode) && checkProgress(config, "Simplifying contours ...")) 998 | return; 999 | 1000 | if (config->enablesmooththresh) 1001 | lsim = linesim(segcropped, LineSimplificationType::DouglasPeucker, config->smooththresh); 1002 | else 1003 | lsim = segcropped.clone(); 1004 | 1005 | if ((!config->batchmode) && checkProgress(config, "Determining distance map ...")) 1006 | return; 1007 | 1008 | dist = bwdist(lsim); 1009 | 1010 | if ((!config->batchmode) && checkProgress(config, "Skeletonizing ...")) 1011 | return; 1012 | 1013 | skel = bwskel(lsim, dist); 1014 | 1015 | if ((!config->batchmode) && checkProgress(config, "Finding the contours ...")) 1016 | return; 1017 | 1018 | findContours(lsim.clone(), contours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE); 1019 | 1020 | // Convex hull is determined only for whole roots. 1021 | if (config->roottype == 0) 1022 | { 1023 | if ((!config->batchmode) && checkProgress(config, "Finding the convex hull ...")) 1024 | return; 1025 | 1026 | hullpt.resize(1); 1027 | if (contours.size() > 0) 1028 | { 1029 | if (config->keepLargest) 1030 | convexHull(contours[0], hullpt[0], false); 1031 | else 1032 | { 1033 | // Combine all the contours before finding the convex hull that 1034 | // encapsulates all the contours. 1035 | size_t sz = 0; 1036 | vector cont; 1037 | for (auto& co : contours) 1038 | sz += co.size(); 1039 | cont.reserve(sz); 1040 | for (auto& co : contours) 1041 | cont.insert(cont.end(), co.begin(), co.end()); 1042 | 1043 | convexHull(cont, hullpt[0], false); 1044 | } 1045 | } 1046 | } 1047 | 1048 | if ((!config->batchmode) && checkProgress(config, "Finding the root topology ...")) 1049 | return; 1050 | 1051 | getroottopology(skel, dist, branchpts, endpts, overlappts, rootsegments, config->enableRootPruning, config->rootPruningThreshold); 1052 | 1053 | if ((!config->batchmode) && checkProgress(config, "Extracting the features ...")) 1054 | return; 1055 | 1056 | #ifndef _DEBUG 1057 | t1 = new thread([&]() { 1058 | #endif 1059 | if (config->roottype == 0) 1060 | { 1061 | getshallowdeeproots(rootsegments, shallowo, mediumo, deepo, avgang); 1062 | 1063 | holes = addBorder(lsim, 0); 1064 | 1065 | holepts = getConnectedComponents(255 - holes, -1, 4); 1066 | nholes = 0; 1067 | avgholesize = 0.0; 1068 | 1069 | for (auto &h : holepts) 1070 | { 1071 | isborder = false; 1072 | 1073 | if (!isborderholefound) 1074 | { 1075 | for (auto &hv : h) 1076 | { 1077 | if (hv == 0) 1078 | { 1079 | isborder = true; 1080 | isborderholefound = true; 1081 | break; 1082 | } 1083 | } 1084 | } 1085 | 1086 | if (!isborder) 1087 | { 1088 | avgholesize += h.size(); 1089 | nholes++; 1090 | } 1091 | } 1092 | 1093 | avgholesize /= nholes; 1094 | 1095 | convarea = 0.0; 1096 | 1097 | 1098 | for (int i = 0, ni = 0; i < hullpt[0].size(); i++) 1099 | { 1100 | ni = ((i + 1) % hullpt[0].size()); 1101 | convarea += double(hullpt[0][i].x * hullpt[0][ni].y - hullpt[0][ni].x * hullpt[0][i].y); 1102 | } 1103 | 1104 | convarea /= 2.0; 1105 | } 1106 | else 1107 | { 1108 | //getrootlength(skel, rootsegments, overlappts, rootlength); 1109 | //getvolumesurfacearea(skel, dist, rootsegments, overlappts, volume, surfacearea); 1110 | 1111 | //getMedianMaxRootNumbers(lsim, mediannoroots, maxnoroots); 1112 | perimeterlength = getperimeterlength(contours) * pixel2mm; 1113 | } 1114 | 1115 | nwarea = double(countNonZero(lsim)); 1116 | 1117 | #ifndef _DEBUG 1118 | }); 1119 | #endif 1120 | // We extract the root length, volume and surface area in a separate 1121 | // thread if the root type we are working is disconnected roots. 1122 | getrootradii(skel, lsim, dist, rootsegments, radii, maxradius, maxradrowidx); 1123 | //if (config->roottype == 0) 1124 | // getrootlength(skel, rootsegments, overlappts, rootlength); 1125 | getavgrootradius(radii, medradius, avgradius); 1126 | //if (config->roottype == 0) 1127 | // getvolumesurfacearea(skel, dist, rootsegments, overlappts, volume, surfacearea); 1128 | 1129 | if (config->batchmode) 1130 | getdiameterrangehistograms(skel, dist, rootsegments, overlappts, radiusranges, rootlengthhist, projareahist, sahist, vhist, rootlength, volume, surfacearea); 1131 | else 1132 | { 1133 | getdiameterrangehistograms(skel, dist, rootsegments, overlappts, radiusranges, rootlengthhist, projareahist, sahist, vhist, rootlength, volume, surfacearea, rtdpoints); 1134 | config->rtdpoints = rtdpoints; 1135 | } 1136 | 1137 | double rmin = 10000, rmax = -1, cmin = 10000, cmax = -1; 1138 | 1139 | if (config->roottype == 0) 1140 | { 1141 | auto fresult = find(lsim > 0, FindType::Subscripts); 1142 | int *rcp = fresult.first.ptr(); 1143 | rmin = fresult.first.rows; 1144 | cmin = fresult.first.rows; 1145 | 1146 | for (int ii = 0; ii < fresult.first.rows; ii++) 1147 | { 1148 | if (rmin > rcp[2 * ii]) 1149 | rmin = rcp[2 * ii]; 1150 | if (cmin > rcp[2 * ii + 1]) 1151 | cmin = rcp[2 * ii + 1]; 1152 | if (rmax < rcp[2 * ii]) 1153 | rmax = rcp[2 * ii]; 1154 | if (cmax < rcp[2 * ii + 1]) 1155 | cmax = rcp[2 * ii + 1]; 1156 | } 1157 | 1158 | rmax++; 1159 | cmax++; 1160 | widthtodepthratio = double(cmax - cmin) / double(rmax - rmin); 1161 | 1162 | getMedianMaxRootNumbers(lsim, mediannoroots, maxnoroots); 1163 | perimeterlength = getperimeterlength(contours) * pixel2mm; 1164 | } 1165 | 1166 | if (maxradius > 0 && lsim.rows > 1 && config->roottype == 0) 1167 | lowerrootarea = double(countNonZero(lsim.rowRange(maxradrowidx, lsim.rows))); 1168 | else 1169 | lowerrootarea = NAN; 1170 | 1171 | #ifndef _DEBUG 1172 | t1->join(); 1173 | 1174 | delete t1; 1175 | #endif 1176 | 1177 | toc(vtime); 1178 | //cout << "Done. Processing time : " << vtime << " seconds." << endl; 1179 | 1180 | 1181 | // File name,Median number of roots,Maximum number of roots,Number of root tips,Total root length, 1182 | // Depth,Maximum width,Width-to-depth ratio,Network area,Convex area,Solidity, 1183 | // Lower Root Area,Average diameter,Median diameter,Maximum diameter, 1184 | // Perimeter,Volume,Surface area, 1185 | // Holes,Average Hole size,Computation,Average root orientation 1186 | // Shallow Angle Frequency,Medium Angle Frequency,Steep Angle Frequency,Shallowness Index, 1187 | // Fine Radius Frequency,Medium Radius Frequency,Coarse Radius Frequency,Fineness Index, 1188 | int featureidx = 0; 1189 | if (config->roottype == 0) 1190 | { 1191 | config->features[featureidx++] = mediannoroots; 1192 | config->features[featureidx++] = maxnoroots; 1193 | } 1194 | config->features[featureidx++] = endpts.size(); 1195 | if (config->roottype != 0) 1196 | config->features[featureidx++] = branchpts.size(); 1197 | config->features[featureidx++] = rootlength * pixel2mm; 1198 | if (config->roottype != 0) 1199 | config->features[featureidx++] = branchpts.size() / (rootlength * pixel2mm); 1200 | if (config->roottype == 0) 1201 | { 1202 | config->features[featureidx++] = double(rmax - rmin) * pixel2mm; 1203 | config->features[featureidx++] = double(cmax - cmin) * pixel2mm; 1204 | config->features[featureidx++] = widthtodepthratio; 1205 | } 1206 | config->features[featureidx++] = nwarea * pixel2mm * pixel2mm; 1207 | if (config->roottype == 0) 1208 | { 1209 | config->features[featureidx++] = convarea * pixel2mm * pixel2mm; 1210 | config->features[featureidx] = config->features[featureidx - 2] / config->features[featureidx - 1]; 1211 | featureidx++; 1212 | config->features[featureidx++] = lowerrootarea * pixel2mm * pixel2mm; 1213 | } 1214 | config->features[featureidx++] = avgradius * pixel2mm * 2.0; 1215 | config->features[featureidx++] = medradius * pixel2mm * 2.0; 1216 | if (maxradius >= 0) 1217 | config->features[featureidx++] = maxradius * pixel2mm * 2.0; 1218 | else 1219 | config->features[featureidx++] = NAN; 1220 | config->features[featureidx++] = perimeterlength; 1221 | config->features[featureidx++] = volume * pixel2mm * pixel2mm * pixel2mm; 1222 | config->features[featureidx++] = surfacearea * pixel2mm * pixel2mm; 1223 | if (config->roottype == 0) 1224 | { 1225 | config->features[featureidx++] = nholes; 1226 | config->features[featureidx++] = avgholesize * pixel2mm * pixel2mm; 1227 | } 1228 | config->features[featureidx++] = vtime; 1229 | if (config->roottype == 0) 1230 | { 1231 | config->features[featureidx++] = avgang; 1232 | config->features[featureidx++] = shallowo; 1233 | config->features[featureidx++] = mediumo; 1234 | config->features[featureidx++] = deepo; 1235 | } 1236 | 1237 | if (!config->batchmode) 1238 | config->rootlengthhist.clear(); 1239 | for (int k = 0; k <= radiusranges.size(); k++) 1240 | { 1241 | config->features[featureidx++] = rootlengthhist[k] * pixel2mm; 1242 | if (!config->batchmode) 1243 | config->rootlengthhist.push_back(rootlengthhist[k] * pixel2mm); 1244 | } 1245 | for (int k = 0; k <= radiusranges.size(); k++) 1246 | config->features[featureidx++] = projareahist[k] * pixel2mm * pixel2mm; 1247 | for (int k = 0; k <= radiusranges.size(); k++) 1248 | config->features[featureidx++] = sahist[k] * pixel2mm * pixel2mm; 1249 | for (int k = 0; k <= radiusranges.size(); k++) 1250 | config->features[featureidx++] = vhist[k] * pixel2mm * pixel2mm * pixel2mm; 1251 | 1252 | if (!config->batchmode) 1253 | config->rtdpoints *= pixel2mm; 1254 | 1255 | if ((!config->batchmode) || (config->batchmode && config->savesegmented)) 1256 | { 1257 | Mat m; 1258 | 1259 | //if (config->invertimage) 1260 | //{ 1261 | m = Mat::zeros(seg.size(), seg.type()); 1262 | lsim.copyTo(m.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg)); 1263 | m = (m < 128); 1264 | //} 1265 | //else 1266 | //{ 1267 | /*m = Mat::zeros(seg.size(), seg.type()); 1268 | lsim.copyTo(m.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg)); 1269 | m = (m < 128);*/ 1270 | //} 1271 | 1272 | //imwrite(sefilename, m); 1273 | if (config->rotation != 0) 1274 | { 1275 | rotate(m, config->seg, revflag); 1276 | } 1277 | else 1278 | { 1279 | m.copyTo(config->seg); 1280 | } 1281 | } 1282 | 1283 | if ((!config->batchmode) && checkProgress(config, "Generating output image ...")) 1284 | return; 1285 | 1286 | if (config->batchmode && !config->saveprocessed) 1287 | return; 1288 | else 1289 | { 1290 | Mat m; 1291 | 1292 | m = Mat::zeros(seg.size(), lsim.type()); 1293 | lsim.copyTo(m.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg)); 1294 | lsim = m.clone(); 1295 | m = Mat::zeros(seg.size(), CV_32FC1); 1296 | dist.copyTo(m.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg)); 1297 | dist = m.clone(); 1298 | m = Mat::zeros(seg.size(), seg.type()); 1299 | skel.copyTo(m.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg)); 1300 | skel = m.clone(); 1301 | } 1302 | 1303 | // Convex hull is drawn on feature images only for whole roots. 1304 | if (config->roottype == 0) 1305 | { 1306 | Mat m = Mat::zeros(seg.size(), lsim.type()); 1307 | 1308 | if (config->showConvexHull) 1309 | { 1310 | hull = Mat::zeros(rmaxseg - rminseg, cmaxseg - cminseg, CV_8UC1); 1311 | drawContours(hull, hullpt, -1, Scalar(255), 2, 8, noArray(), 0, Point()); 1312 | hull.copyTo(m.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg)); 1313 | } 1314 | 1315 | hull = m.clone(); 1316 | 1317 | if (config->showConvexHull) 1318 | dilate(hull, dilatedhull, getStructuringElement(MORPH_ELLIPSE, Size(3, 3))); 1319 | } 1320 | 1321 | Mat m = Mat::zeros(seg.size(), lsim.type()); 1322 | 1323 | if (config->showContours) 1324 | { 1325 | perimeter = Mat::zeros(rmaxseg - rminseg, cmaxseg - cminseg, CV_8UC1); 1326 | drawContours(perimeter, contours, -1, Scalar(255), config->contourwidth, 8, hierarchy); 1327 | perimeter.copyTo(m.rowRange(rminseg, rmaxseg).colRange(cminseg, cmaxseg)); 1328 | } 1329 | 1330 | perimeter = m.clone(); 1331 | 1332 | // Invert the color so the background is white 1333 | lsim = (lsim < 128); 1334 | 1335 | // Convert distance transform to an image. 1336 | double minv, maxv; 1337 | dist.copyTo(m); 1338 | minMaxLoc(m, &minv, &maxv); 1339 | m = (m / maxv) * 255; 1340 | m.convertTo(m, CV_8UC1); 1341 | // To dilate skel, perimeter and convex hull. 1342 | 1343 | /*sefilename = config->savefolder + fefile.substr(0, fefile.length() - 4) + "_seg6.png"; 1344 | img2 = drawtopology2(lsim, skel, branchpts, endpts, overlappts); 1345 | img2 = img2.rowRange(rmi, rma).colRange(cmi, cma).clone(); 1346 | imwrite(sefilename, img2);*/ 1347 | if (config->roottype == 0) 1348 | { 1349 | if (config->showMedialAxis && (!config->showMedialAxisDiameter)) 1350 | { 1351 | //skel = skel + perimeter; 1352 | selement = getStructuringElement(MORPH_ELLIPSE, Size(config->medialaxiswidth, config->medialaxiswidth)); 1353 | dilate(skel, dilatedskel, selement); 1354 | //dilate(hull, dilatedhull, selement); 1355 | dilatedskel = dilatedskel + perimeter; 1356 | } 1357 | else 1358 | dilatedskel = perimeter; 1359 | 1360 | Mat dskel; 1361 | 1362 | channels.push_back(lsim - dilatedskel); 1363 | 1364 | if (config->showDistMap) 1365 | channels.push_back(lsim - dilatedskel - dilatedhull + m); 1366 | else 1367 | channels.push_back(lsim - dilatedskel - dilatedhull); 1368 | 1369 | channels.push_back((lsim - dilatedhull - dilatedskel) + dilatedskel); 1370 | 1371 | if (config->showMedialAxisDiameter) 1372 | { 1373 | vector dch; 1374 | dskel = drawmedialaxis(dist, skel, radiusranges, config->medialaxiswidth); 1375 | split(dskel, dch); 1376 | 1377 | auto t = (dch[1] > 0); 1378 | 1379 | // We subtract the green channel of the medial axis 1380 | // to set the medial axis pixels to zero 1381 | for (int cidx = 0; cidx < channels.size(); cidx++) 1382 | { 1383 | channels[cidx] = channels[cidx] - t; 1384 | channels[cidx] = channels[cidx] + dch[cidx]; 1385 | } 1386 | } 1387 | 1388 | merge(channels, merged); 1389 | 1390 | holes = lsim - dilatedskel; 1391 | holes = addBorder(255 - holes, 0); 1392 | 1393 | if (holepts.size() <= 1) 1394 | { 1395 | ////merged = drawtopology2(lsim, skel, branchpts, endpts, overlappts); 1396 | //imwrite(fefilename, merged); 1397 | cvtColor(merged, merged, COLOR_BGR2RGB); 1398 | if (config->rotation != 0) 1399 | { 1400 | rotate(merged, config->processed, revflag); 1401 | } 1402 | else 1403 | { 1404 | merged.copyTo(config->processed); 1405 | } 1406 | 1407 | return; 1408 | } 1409 | 1410 | if (config->showHoles) 1411 | { 1412 | holepts = getholes(holepts, Size(cmaxseg - cminseg + 2, rmaxseg - rminseg + 2)); 1413 | if (holepts.size() > 5) 1414 | { 1415 | centroids = getComponentCentroid(holepts, holes.size()); 1416 | pmap = pdist2(centroids, holes.size()); 1417 | nearest = getnearestcomponents(pmap); 1418 | colorcodes = getcolorcodes(nearest); 1419 | } 1420 | else 1421 | { 1422 | vector colvalues = { 1,2,3,4,5 }; 1423 | std::shuffle(colvalues.begin(), colvalues.end(), urng); 1424 | colorcodes.resize(holepts.size()); 1425 | 1426 | for (int i = 0; i < colorcodes.size(); i++) 1427 | colorcodes[i] = colvalues[i]; 1428 | } 1429 | 1430 | merged = drawtopology_wholeroot(merged, Scalar_(rmaxseg, rminseg, cmaxseg, cminseg), holepts, colorcodes, colors); 1431 | } 1432 | } 1433 | else 1434 | { 1435 | if (config->showMedialAxis) 1436 | { 1437 | selement = getStructuringElement(MORPH_ELLIPSE, Size(config->medialaxiswidth, config->medialaxiswidth)); 1438 | dilate(skel, dilatedskel, selement); 1439 | } 1440 | else 1441 | { 1442 | skel = Mat::zeros(lsim.size(), CV_8UC1); 1443 | dilatedskel = Mat::zeros(lsim.size(), CV_8UC1); 1444 | branchpts.clear(); 1445 | endpts.clear(); 1446 | overlappts.clear(); 1447 | } 1448 | 1449 | Mat dmap; 1450 | if (config->showDistMap) 1451 | dmap = m; 1452 | else 1453 | dmap = Mat::zeros(lsim.size(), CV_8UC1); 1454 | 1455 | if (config->showMedialAxis) 1456 | { 1457 | if (!config->showMedialAxisDiameter) 1458 | merged = drawtopology_disconnectedroot(lsim, dmap, Scalar_(rmaxseg, rminseg, cmaxseg, cminseg), dilatedskel, branchpts, endpts, overlappts, config->medialaxiswidth); 1459 | else 1460 | { 1461 | vector lch; 1462 | lch.push_back(lsim - dilatedskel); 1463 | lch.push_back(lsim + dmap - dilatedskel); 1464 | lch.push_back(lsim - dilatedskel); 1465 | merge(lch, merged); 1466 | 1467 | Mat dskel = drawmedialaxis(dist, skel, radiusranges, config->medialaxiswidth); 1468 | merged = merged + dskel; 1469 | //vector dch; 1470 | //split(dskel, dch); 1471 | 1472 | //auto t = (dch[0] > 0); 1473 | // 1474 | 1475 | //// We subtract the green channel of the medial axis 1476 | //// to set the medial axis pixels to zero 1477 | //for (int cidx = 0; cidx < lch.size(); cidx++) 1478 | //{ 1479 | // lch[cidx] = lch[cidx] - t; 1480 | // window("adad", t); 1481 | // window("adad2", dch[cidx]); 1482 | // lch[cidx] = lch[cidx] + dch[cidx]; 1483 | // window("adad3", lch[cidx]); 1484 | //} 1485 | 1486 | 1487 | //cvtColor(merged, merged, COLOR_BGR2RGB); 1488 | } 1489 | } 1490 | else 1491 | { 1492 | vector lch; 1493 | lch.push_back(lsim - dilatedskel); 1494 | lch.push_back(lsim + dmap - dilatedskel); 1495 | lch.push_back(lsim - dilatedskel); 1496 | merge(lch, merged); 1497 | } 1498 | } 1499 | 1500 | cvtColor(merged, merged, COLOR_BGR2RGB); 1501 | 1502 | if (config->rotation != 0) 1503 | { 1504 | rotate(merged, config->processed, revflag); 1505 | } 1506 | else 1507 | { 1508 | merged.copyTo(config->processed); 1509 | } 1510 | 1511 | //merged.copyTo(config->processed); 1512 | //imwrite(fefilename, merged); 1513 | } 1514 | 1515 | int main(int argc, char *argv[]) 1516 | { 1517 | setUseOptimized(true); 1518 | 1519 | if (!checkHardwareSupport(CV_CPU_AVX2)) 1520 | { 1521 | init(argc, argv, false); 1522 | setUseOptimized(false); 1523 | } 1524 | else 1525 | { 1526 | init(argc, argv, true); 1527 | } 1528 | 1529 | //QApplication::setAttribute(Qt::AA_EnableHighDpiScaling); 1530 | 1531 | QCoreApplication *app = QApplication::instance(); 1532 | app->setApplicationName("RhizoVision Explorer"); 1533 | 1534 | Ptr wnd = getImageProcessorWindow(QIcon(":/icons/RVElogoclearback.png")); 1535 | wnd->enableROI(true); 1536 | wnd->setVisibleROI(true); 1537 | wnd->enableActions(true); 1538 | wnd->setVisibleActions(true); 1539 | wnd->setInitialBanner(QPixmap(":/icons/RVElogoclearback.png").scaledToHeight(200, Qt::SmoothTransformation), 1540 | QPixmap(), //QPixmap(":/icons/noble-logo-color.png").scaledToHeight(75, Qt::SmoothTransformation), 1541 | "RhizoVision Explorer", 1542 | "Load a plant root image from File menu\n or drag and drop it here."); 1543 | MainUI *dialog = new MainUI(); 1544 | dialog->setprocessfunction(feature_extractor); 1545 | dialog->setHostWindow(wnd.get()); 1546 | 1547 | QObject::connect(dialog, &MainUI::updateVisualOutput, [&](Mat m) { wnd->setImage(m); }); 1548 | //QObject::connect(dialog, &MainUI::updateProgress, [&](QString status) { wnd->updateProgress(status); }); 1549 | 1550 | wnd->loadPlugins(dialog); 1551 | wnd->show(); 1552 | 1553 | return QApplication::exec(); 1554 | } 1555 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/moc_FeatureExtractorThread.cpp: -------------------------------------------------------------------------------- 1 | /**************************************************************************** 2 | ** Meta object code from reading C++ file 'FeatureExtractorThread.h' 3 | ** 4 | ** Created by: The Qt Meta Object Compiler version 67 (Qt 5.12.3) 5 | ** 6 | ** WARNING! All changes made in this file will be lost! 7 | *****************************************************************************/ 8 | 9 | #include "FeatureExtractorThread.h" 10 | #include 11 | #include 12 | #if !defined(Q_MOC_OUTPUT_REVISION) 13 | #error "The header file 'FeatureExtractorThread.h' doesn't include ." 14 | #elif Q_MOC_OUTPUT_REVISION != 67 15 | #error "This file was generated using the moc from 5.12.3. It" 16 | #error "cannot be used with the include files from this version of Qt." 17 | #error "(The moc has changed too much.)" 18 | #endif 19 | 20 | QT_BEGIN_MOC_NAMESPACE 21 | QT_WARNING_PUSH 22 | QT_WARNING_DISABLE_DEPRECATED 23 | struct qt_meta_stringdata_FeatureExtractorThread_t { 24 | QByteArrayData data[5]; 25 | char stringdata0[55]; 26 | }; 27 | #define QT_MOC_LITERAL(idx, ofs, len) \ 28 | Q_STATIC_BYTE_ARRAY_DATA_HEADER_INITIALIZER_WITH_OFFSET(len, \ 29 | qptrdiff(offsetof(qt_meta_stringdata_FeatureExtractorThread_t, stringdata0) + ofs \ 30 | - idx * sizeof(QByteArrayData)) \ 31 | ) 32 | static const qt_meta_stringdata_FeatureExtractorThread_t qt_meta_stringdata_FeatureExtractorThread = { 33 | { 34 | QT_MOC_LITERAL(0, 0, 22), // "FeatureExtractorThread" 35 | QT_MOC_LITERAL(1, 23, 14), // "ReportProgress" 36 | QT_MOC_LITERAL(2, 38, 0), // "" 37 | QT_MOC_LITERAL(3, 39, 8), // "filename" 38 | QT_MOC_LITERAL(4, 48, 6) // "fileno" 39 | 40 | }, 41 | "FeatureExtractorThread\0ReportProgress\0" 42 | "\0filename\0fileno" 43 | }; 44 | #undef QT_MOC_LITERAL 45 | 46 | static const uint qt_meta_data_FeatureExtractorThread[] = { 47 | 48 | // content: 49 | 8, // revision 50 | 0, // classname 51 | 0, 0, // classinfo 52 | 1, 14, // methods 53 | 0, 0, // properties 54 | 0, 0, // enums/sets 55 | 0, 0, // constructors 56 | 0, // flags 57 | 1, // signalCount 58 | 59 | // signals: name, argc, parameters, tag, flags 60 | 1, 2, 19, 2, 0x06 /* Public */, 61 | 62 | // signals: parameters 63 | QMetaType::Void, QMetaType::QString, QMetaType::Int, 3, 4, 64 | 65 | 0 // eod 66 | }; 67 | 68 | void FeatureExtractorThread::qt_static_metacall(QObject *_o, QMetaObject::Call _c, int _id, void **_a) 69 | { 70 | if (_c == QMetaObject::InvokeMetaMethod) { 71 | auto *_t = static_cast(_o); 72 | Q_UNUSED(_t) 73 | switch (_id) { 74 | case 0: _t->ReportProgress((*reinterpret_cast< QString(*)>(_a[1])),(*reinterpret_cast< int(*)>(_a[2]))); break; 75 | default: ; 76 | } 77 | } else if (_c == QMetaObject::IndexOfMethod) { 78 | int *result = reinterpret_cast(_a[0]); 79 | { 80 | using _t = void (FeatureExtractorThread::*)(QString , int ); 81 | if (*reinterpret_cast<_t *>(_a[1]) == static_cast<_t>(&FeatureExtractorThread::ReportProgress)) { 82 | *result = 0; 83 | return; 84 | } 85 | } 86 | } 87 | } 88 | 89 | QT_INIT_METAOBJECT const QMetaObject FeatureExtractorThread::staticMetaObject = { { 90 | &QThread::staticMetaObject, 91 | qt_meta_stringdata_FeatureExtractorThread.data, 92 | qt_meta_data_FeatureExtractorThread, 93 | qt_static_metacall, 94 | nullptr, 95 | nullptr 96 | } }; 97 | 98 | 99 | const QMetaObject *FeatureExtractorThread::metaObject() const 100 | { 101 | return QObject::d_ptr->metaObject ? QObject::d_ptr->dynamicMetaObject() : &staticMetaObject; 102 | } 103 | 104 | void *FeatureExtractorThread::qt_metacast(const char *_clname) 105 | { 106 | if (!_clname) return nullptr; 107 | if (!strcmp(_clname, qt_meta_stringdata_FeatureExtractorThread.stringdata0)) 108 | return static_cast(this); 109 | return QThread::qt_metacast(_clname); 110 | } 111 | 112 | int FeatureExtractorThread::qt_metacall(QMetaObject::Call _c, int _id, void **_a) 113 | { 114 | _id = QThread::qt_metacall(_c, _id, _a); 115 | if (_id < 0) 116 | return _id; 117 | if (_c == QMetaObject::InvokeMetaMethod) { 118 | if (_id < 1) 119 | qt_static_metacall(this, _c, _id, _a); 120 | _id -= 1; 121 | } else if (_c == QMetaObject::RegisterMethodArgumentMetaType) { 122 | if (_id < 1) 123 | *reinterpret_cast(_a[0]) = -1; 124 | _id -= 1; 125 | } 126 | return _id; 127 | } 128 | 129 | // SIGNAL 0 130 | void FeatureExtractorThread::ReportProgress(QString _t1, int _t2) 131 | { 132 | void *_a[] = { nullptr, const_cast(reinterpret_cast(&_t1)), const_cast(reinterpret_cast(&_t2)) }; 133 | QMetaObject::activate(this, &staticMetaObject, 0, _a); 134 | } 135 | QT_WARNING_POP 136 | QT_END_MOC_NAMESPACE 137 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/moc_MainUI.cpp: -------------------------------------------------------------------------------- 1 | /**************************************************************************** 2 | ** Meta object code from reading C++ file 'MainUI.h' 3 | ** 4 | ** Created by: The Qt Meta Object Compiler version 67 (Qt 5.12.3) 5 | ** 6 | ** WARNING! All changes made in this file will be lost! 7 | *****************************************************************************/ 8 | 9 | #include "MainUI.h" 10 | #include 11 | #include 12 | #include 13 | #if !defined(Q_MOC_OUTPUT_REVISION) 14 | #error "The header file 'MainUI.h' doesn't include ." 15 | #elif Q_MOC_OUTPUT_REVISION != 67 16 | #error "This file was generated using the moc from 5.12.3. It" 17 | #error "cannot be used with the include files from this version of Qt." 18 | #error "(The moc has changed too much.)" 19 | #endif 20 | 21 | QT_BEGIN_MOC_NAMESPACE 22 | QT_WARNING_PUSH 23 | QT_WARNING_DISABLE_DEPRECATED 24 | struct qt_meta_stringdata_CheckEnabler_t { 25 | QByteArrayData data[4]; 26 | char stringdata0[39]; 27 | }; 28 | #define QT_MOC_LITERAL(idx, ofs, len) \ 29 | Q_STATIC_BYTE_ARRAY_DATA_HEADER_INITIALIZER_WITH_OFFSET(len, \ 30 | qptrdiff(offsetof(qt_meta_stringdata_CheckEnabler_t, stringdata0) + ofs \ 31 | - idx * sizeof(QByteArrayData)) \ 32 | ) 33 | static const qt_meta_stringdata_CheckEnabler_t qt_meta_stringdata_CheckEnabler = { 34 | { 35 | QT_MOC_LITERAL(0, 0, 12), // "CheckEnabler" 36 | QT_MOC_LITERAL(1, 13, 12), // "stateChanged" 37 | QT_MOC_LITERAL(2, 26, 0), // "" 38 | QT_MOC_LITERAL(3, 27, 11) // "textChanged" 39 | 40 | }, 41 | "CheckEnabler\0stateChanged\0\0textChanged" 42 | }; 43 | #undef QT_MOC_LITERAL 44 | 45 | static const uint qt_meta_data_CheckEnabler[] = { 46 | 47 | // content: 48 | 8, // revision 49 | 0, // classname 50 | 0, 0, // classinfo 51 | 2, 14, // methods 52 | 0, 0, // properties 53 | 0, 0, // enums/sets 54 | 0, 0, // constructors 55 | 0, // flags 56 | 2, // signalCount 57 | 58 | // signals: name, argc, parameters, tag, flags 59 | 1, 0, 24, 2, 0x06 /* Public */, 60 | 3, 0, 25, 2, 0x06 /* Public */, 61 | 62 | // signals: parameters 63 | QMetaType::Void, 64 | QMetaType::Void, 65 | 66 | 0 // eod 67 | }; 68 | 69 | void CheckEnabler::qt_static_metacall(QObject *_o, QMetaObject::Call _c, int _id, void **_a) 70 | { 71 | if (_c == QMetaObject::InvokeMetaMethod) { 72 | auto *_t = static_cast(_o); 73 | Q_UNUSED(_t) 74 | switch (_id) { 75 | case 0: _t->stateChanged(); break; 76 | case 1: _t->textChanged(); break; 77 | default: ; 78 | } 79 | } else if (_c == QMetaObject::IndexOfMethod) { 80 | int *result = reinterpret_cast(_a[0]); 81 | { 82 | using _t = void (CheckEnabler::*)(); 83 | if (*reinterpret_cast<_t *>(_a[1]) == static_cast<_t>(&CheckEnabler::stateChanged)) { 84 | *result = 0; 85 | return; 86 | } 87 | } 88 | { 89 | using _t = void (CheckEnabler::*)(); 90 | if (*reinterpret_cast<_t *>(_a[1]) == static_cast<_t>(&CheckEnabler::textChanged)) { 91 | *result = 1; 92 | return; 93 | } 94 | } 95 | } 96 | Q_UNUSED(_a); 97 | } 98 | 99 | QT_INIT_METAOBJECT const QMetaObject CheckEnabler::staticMetaObject = { { 100 | &QWidget::staticMetaObject, 101 | qt_meta_stringdata_CheckEnabler.data, 102 | qt_meta_data_CheckEnabler, 103 | qt_static_metacall, 104 | nullptr, 105 | nullptr 106 | } }; 107 | 108 | 109 | const QMetaObject *CheckEnabler::metaObject() const 110 | { 111 | return QObject::d_ptr->metaObject ? QObject::d_ptr->dynamicMetaObject() : &staticMetaObject; 112 | } 113 | 114 | void *CheckEnabler::qt_metacast(const char *_clname) 115 | { 116 | if (!_clname) return nullptr; 117 | if (!strcmp(_clname, qt_meta_stringdata_CheckEnabler.stringdata0)) 118 | return static_cast(this); 119 | return QWidget::qt_metacast(_clname); 120 | } 121 | 122 | int CheckEnabler::qt_metacall(QMetaObject::Call _c, int _id, void **_a) 123 | { 124 | _id = QWidget::qt_metacall(_c, _id, _a); 125 | if (_id < 0) 126 | return _id; 127 | if (_c == QMetaObject::InvokeMetaMethod) { 128 | if (_id < 2) 129 | qt_static_metacall(this, _c, _id, _a); 130 | _id -= 2; 131 | } else if (_c == QMetaObject::RegisterMethodArgumentMetaType) { 132 | if (_id < 2) 133 | *reinterpret_cast(_a[0]) = -1; 134 | _id -= 2; 135 | } 136 | return _id; 137 | } 138 | 139 | // SIGNAL 0 140 | void CheckEnabler::stateChanged() 141 | { 142 | QMetaObject::activate(this, &staticMetaObject, 0, nullptr); 143 | } 144 | 145 | // SIGNAL 1 146 | void CheckEnabler::textChanged() 147 | { 148 | QMetaObject::activate(this, &staticMetaObject, 1, nullptr); 149 | } 150 | struct qt_meta_stringdata_StringCheckEnabler_t { 151 | QByteArrayData data[4]; 152 | char stringdata0[45]; 153 | }; 154 | #define QT_MOC_LITERAL(idx, ofs, len) \ 155 | Q_STATIC_BYTE_ARRAY_DATA_HEADER_INITIALIZER_WITH_OFFSET(len, \ 156 | qptrdiff(offsetof(qt_meta_stringdata_StringCheckEnabler_t, stringdata0) + ofs \ 157 | - idx * sizeof(QByteArrayData)) \ 158 | ) 159 | static const qt_meta_stringdata_StringCheckEnabler_t qt_meta_stringdata_StringCheckEnabler = { 160 | { 161 | QT_MOC_LITERAL(0, 0, 18), // "StringCheckEnabler" 162 | QT_MOC_LITERAL(1, 19, 12), // "stateChanged" 163 | QT_MOC_LITERAL(2, 32, 0), // "" 164 | QT_MOC_LITERAL(3, 33, 11) // "textChanged" 165 | 166 | }, 167 | "StringCheckEnabler\0stateChanged\0\0" 168 | "textChanged" 169 | }; 170 | #undef QT_MOC_LITERAL 171 | 172 | static const uint qt_meta_data_StringCheckEnabler[] = { 173 | 174 | // content: 175 | 8, // revision 176 | 0, // classname 177 | 0, 0, // classinfo 178 | 2, 14, // methods 179 | 0, 0, // properties 180 | 0, 0, // enums/sets 181 | 0, 0, // constructors 182 | 0, // flags 183 | 2, // signalCount 184 | 185 | // signals: name, argc, parameters, tag, flags 186 | 1, 0, 24, 2, 0x06 /* Public */, 187 | 3, 0, 25, 2, 0x06 /* Public */, 188 | 189 | // signals: parameters 190 | QMetaType::Void, 191 | QMetaType::Void, 192 | 193 | 0 // eod 194 | }; 195 | 196 | void StringCheckEnabler::qt_static_metacall(QObject *_o, QMetaObject::Call _c, int _id, void **_a) 197 | { 198 | if (_c == QMetaObject::InvokeMetaMethod) { 199 | auto *_t = static_cast(_o); 200 | Q_UNUSED(_t) 201 | switch (_id) { 202 | case 0: _t->stateChanged(); break; 203 | case 1: _t->textChanged(); break; 204 | default: ; 205 | } 206 | } else if (_c == QMetaObject::IndexOfMethod) { 207 | int *result = reinterpret_cast(_a[0]); 208 | { 209 | using _t = void (StringCheckEnabler::*)(); 210 | if (*reinterpret_cast<_t *>(_a[1]) == static_cast<_t>(&StringCheckEnabler::stateChanged)) { 211 | *result = 0; 212 | return; 213 | } 214 | } 215 | { 216 | using _t = void (StringCheckEnabler::*)(); 217 | if (*reinterpret_cast<_t *>(_a[1]) == static_cast<_t>(&StringCheckEnabler::textChanged)) { 218 | *result = 1; 219 | return; 220 | } 221 | } 222 | } 223 | Q_UNUSED(_a); 224 | } 225 | 226 | QT_INIT_METAOBJECT const QMetaObject StringCheckEnabler::staticMetaObject = { { 227 | &QWidget::staticMetaObject, 228 | qt_meta_stringdata_StringCheckEnabler.data, 229 | qt_meta_data_StringCheckEnabler, 230 | qt_static_metacall, 231 | nullptr, 232 | nullptr 233 | } }; 234 | 235 | 236 | const QMetaObject *StringCheckEnabler::metaObject() const 237 | { 238 | return QObject::d_ptr->metaObject ? QObject::d_ptr->dynamicMetaObject() : &staticMetaObject; 239 | } 240 | 241 | void *StringCheckEnabler::qt_metacast(const char *_clname) 242 | { 243 | if (!_clname) return nullptr; 244 | if (!strcmp(_clname, qt_meta_stringdata_StringCheckEnabler.stringdata0)) 245 | return static_cast(this); 246 | return QWidget::qt_metacast(_clname); 247 | } 248 | 249 | int StringCheckEnabler::qt_metacall(QMetaObject::Call _c, int _id, void **_a) 250 | { 251 | _id = QWidget::qt_metacall(_c, _id, _a); 252 | if (_id < 0) 253 | return _id; 254 | if (_c == QMetaObject::InvokeMetaMethod) { 255 | if (_id < 2) 256 | qt_static_metacall(this, _c, _id, _a); 257 | _id -= 2; 258 | } else if (_c == QMetaObject::RegisterMethodArgumentMetaType) { 259 | if (_id < 2) 260 | *reinterpret_cast(_a[0]) = -1; 261 | _id -= 2; 262 | } 263 | return _id; 264 | } 265 | 266 | // SIGNAL 0 267 | void StringCheckEnabler::stateChanged() 268 | { 269 | QMetaObject::activate(this, &staticMetaObject, 0, nullptr); 270 | } 271 | 272 | // SIGNAL 1 273 | void StringCheckEnabler::textChanged() 274 | { 275 | QMetaObject::activate(this, &staticMetaObject, 1, nullptr); 276 | } 277 | struct qt_meta_stringdata_MainUI_t { 278 | QByteArrayData data[48]; 279 | char stringdata0[569]; 280 | }; 281 | #define QT_MOC_LITERAL(idx, ofs, len) \ 282 | Q_STATIC_BYTE_ARRAY_DATA_HEADER_INITIALIZER_WITH_OFFSET(len, \ 283 | qptrdiff(offsetof(qt_meta_stringdata_MainUI_t, stringdata0) + ofs \ 284 | - idx * sizeof(QByteArrayData)) \ 285 | ) 286 | static const qt_meta_stringdata_MainUI_t qt_meta_stringdata_MainUI = { 287 | { 288 | QT_MOC_LITERAL(0, 0, 6), // "MainUI" 289 | QT_MOC_LITERAL(1, 7, 18), // "updateVisualOutput" 290 | QT_MOC_LITERAL(2, 26, 0), // "" 291 | QT_MOC_LITERAL(3, 27, 7), // "cv::Mat" 292 | QT_MOC_LITERAL(4, 35, 1), // "m" 293 | QT_MOC_LITERAL(5, 37, 14), // "updateProgress" 294 | QT_MOC_LITERAL(6, 52, 6), // "status" 295 | QT_MOC_LITERAL(7, 59, 7), // "getName" 296 | QT_MOC_LITERAL(8, 67, 11), // "std::string" 297 | QT_MOC_LITERAL(9, 79, 18), // "getApplicationType" 298 | QT_MOC_LITERAL(10, 98, 7), // "AppType" 299 | QT_MOC_LITERAL(11, 106, 13), // "getOutputType" 300 | QT_MOC_LITERAL(12, 120, 10), // "OutputType" 301 | QT_MOC_LITERAL(13, 131, 16), // "getAlgorithmName" 302 | QT_MOC_LITERAL(14, 148, 13), // "getParameters" 303 | QT_MOC_LITERAL(15, 162, 28), // "std::vector" 304 | QT_MOC_LITERAL(16, 191, 11), // "getPluginUI" 305 | QT_MOC_LITERAL(17, 203, 8), // "QWidget*" 306 | QT_MOC_LITERAL(18, 212, 8), // "setImage" 307 | QT_MOC_LITERAL(19, 221, 5), // "image" 308 | QT_MOC_LITERAL(20, 227, 9), // "imagename" 309 | QT_MOC_LITERAL(21, 237, 7), // "execute" 310 | QT_MOC_LITERAL(22, 245, 15), // "getOutputImages" 311 | QT_MOC_LITERAL(23, 261, 20), // "std::vector" 312 | QT_MOC_LITERAL(24, 282, 15), // "getDisplayIndex" 313 | QT_MOC_LITERAL(25, 298, 15), // "setDisplayIndex" 314 | QT_MOC_LITERAL(26, 314, 3), // "idx" 315 | QT_MOC_LITERAL(27, 318, 11), // "getFeatures" 316 | QT_MOC_LITERAL(28, 330, 19), // "std::vector" 317 | QT_MOC_LITERAL(29, 350, 6), // "roiidx" 318 | QT_MOC_LITERAL(30, 357, 12), // "setBatchMode" 319 | QT_MOC_LITERAL(31, 370, 2), // "on" 320 | QT_MOC_LITERAL(32, 373, 10), // "saveOutput" 321 | QT_MOC_LITERAL(33, 384, 6), // "savloc" 322 | QT_MOC_LITERAL(34, 391, 13), // "inputfilename" 323 | QT_MOC_LITERAL(35, 405, 12), // "saveMetadata" 324 | QT_MOC_LITERAL(36, 418, 6), // "imgloc" 325 | QT_MOC_LITERAL(37, 425, 8), // "filepath" 326 | QT_MOC_LITERAL(38, 434, 12), // "loadMetadata" 327 | QT_MOC_LITERAL(39, 447, 11), // "writeHeader" 328 | QT_MOC_LITERAL(40, 459, 8), // "filename" 329 | QT_MOC_LITERAL(41, 468, 17), // "getCSVColumnNames" 330 | QT_MOC_LITERAL(42, 486, 20), // "std::vector" 331 | QT_MOC_LITERAL(43, 507, 16), // "getProgressSteps" 332 | QT_MOC_LITERAL(44, 524, 5), // "abort" 333 | QT_MOC_LITERAL(45, 530, 8), // "getChart" 334 | QT_MOC_LITERAL(46, 539, 7), // "QChart*" 335 | QT_MOC_LITERAL(47, 547, 21) // "updatesegmentedoutput" 336 | 337 | }, 338 | "MainUI\0updateVisualOutput\0\0cv::Mat\0m\0" 339 | "updateProgress\0status\0getName\0std::string\0" 340 | "getApplicationType\0AppType\0getOutputType\0" 341 | "OutputType\0getAlgorithmName\0getParameters\0" 342 | "std::vector\0getPluginUI\0" 343 | "QWidget*\0setImage\0image\0imagename\0" 344 | "execute\0getOutputImages\0std::vector\0" 345 | "getDisplayIndex\0setDisplayIndex\0idx\0" 346 | "getFeatures\0std::vector\0roiidx\0" 347 | "setBatchMode\0on\0saveOutput\0savloc\0" 348 | "inputfilename\0saveMetadata\0imgloc\0" 349 | "filepath\0loadMetadata\0writeHeader\0" 350 | "filename\0getCSVColumnNames\0" 351 | "std::vector\0getProgressSteps\0" 352 | "abort\0getChart\0QChart*\0updatesegmentedoutput" 353 | }; 354 | #undef QT_MOC_LITERAL 355 | 356 | static const uint qt_meta_data_MainUI[] = { 357 | 358 | // content: 359 | 8, // revision 360 | 0, // classname 361 | 0, 0, // classinfo 362 | 28, 14, // methods 363 | 0, 0, // properties 364 | 0, 0, // enums/sets 365 | 0, 0, // constructors 366 | 0, // flags 367 | 2, // signalCount 368 | 369 | // signals: name, argc, parameters, tag, flags 370 | 1, 1, 154, 2, 0x06 /* Public */, 371 | 5, 1, 157, 2, 0x06 /* Public */, 372 | 373 | // slots: name, argc, parameters, tag, flags 374 | 7, 0, 160, 2, 0x0a /* Public */, 375 | 9, 0, 161, 2, 0x0a /* Public */, 376 | 11, 0, 162, 2, 0x0a /* Public */, 377 | 13, 0, 163, 2, 0x0a /* Public */, 378 | 14, 0, 164, 2, 0x0a /* Public */, 379 | 16, 0, 165, 2, 0x0a /* Public */, 380 | 18, 2, 166, 2, 0x0a /* Public */, 381 | 18, 1, 171, 2, 0x2a /* Public | MethodCloned */, 382 | 21, 0, 174, 2, 0x0a /* Public */, 383 | 22, 0, 175, 2, 0x0a /* Public */, 384 | 24, 0, 176, 2, 0x0a /* Public */, 385 | 25, 1, 177, 2, 0x0a /* Public */, 386 | 27, 0, 180, 2, 0x0a /* Public */, 387 | 27, 1, 181, 2, 0x0a /* Public */, 388 | 30, 1, 184, 2, 0x0a /* Public */, 389 | 32, 2, 187, 2, 0x0a /* Public */, 390 | 35, 3, 192, 2, 0x0a /* Public */, 391 | 35, 2, 199, 2, 0x2a /* Public | MethodCloned */, 392 | 38, 1, 204, 2, 0x0a /* Public */, 393 | 39, 2, 207, 2, 0x0a /* Public */, 394 | 39, 1, 212, 2, 0x2a /* Public | MethodCloned */, 395 | 41, 0, 215, 2, 0x0a /* Public */, 396 | 43, 0, 216, 2, 0x0a /* Public */, 397 | 44, 0, 217, 2, 0x0a /* Public */, 398 | 45, 0, 218, 2, 0x0a /* Public */, 399 | 47, 0, 219, 2, 0x08 /* Private */, 400 | 401 | // signals: parameters 402 | QMetaType::Void, 0x80000000 | 3, 4, 403 | QMetaType::Void, QMetaType::QString, 6, 404 | 405 | // slots: parameters 406 | 0x80000000 | 8, 407 | 0x80000000 | 10, 408 | 0x80000000 | 12, 409 | 0x80000000 | 8, 410 | 0x80000000 | 15, 411 | 0x80000000 | 17, 412 | QMetaType::Void, 0x80000000 | 3, QMetaType::QString, 19, 20, 413 | QMetaType::Void, 0x80000000 | 3, 19, 414 | QMetaType::Void, 415 | 0x80000000 | 23, 416 | QMetaType::Int, 417 | QMetaType::Void, QMetaType::Int, 26, 418 | 0x80000000 | 28, 419 | 0x80000000 | 28, QMetaType::Int, 29, 420 | QMetaType::Void, QMetaType::Bool, 31, 421 | QMetaType::Int, QMetaType::QString, QMetaType::QString, 33, 34, 422 | QMetaType::Void, QMetaType::QString, QMetaType::QString, QMetaType::QString, 36, 33, 37, 423 | QMetaType::Void, QMetaType::QString, QMetaType::QString, 36, 33, 424 | QMetaType::Void, QMetaType::QString, 37, 425 | QMetaType::Int, QMetaType::QString, QMetaType::QString, 33, 40, 426 | QMetaType::Int, QMetaType::QString, 33, 427 | 0x80000000 | 42, 428 | QMetaType::Int, 429 | QMetaType::Void, 430 | 0x80000000 | 46, 431 | QMetaType::Void, 432 | 433 | 0 // eod 434 | }; 435 | 436 | void MainUI::qt_static_metacall(QObject *_o, QMetaObject::Call _c, int _id, void **_a) 437 | { 438 | if (_c == QMetaObject::InvokeMetaMethod) { 439 | auto *_t = static_cast(_o); 440 | Q_UNUSED(_t) 441 | switch (_id) { 442 | case 0: _t->updateVisualOutput((*reinterpret_cast< cv::Mat(*)>(_a[1]))); break; 443 | case 1: _t->updateProgress((*reinterpret_cast< QString(*)>(_a[1]))); break; 444 | case 2: { std::string _r = _t->getName(); 445 | if (_a[0]) *reinterpret_cast< std::string*>(_a[0]) = std::move(_r); } break; 446 | case 3: { AppType _r = _t->getApplicationType(); 447 | if (_a[0]) *reinterpret_cast< AppType*>(_a[0]) = std::move(_r); } break; 448 | case 4: { OutputType _r = _t->getOutputType(); 449 | if (_a[0]) *reinterpret_cast< OutputType*>(_a[0]) = std::move(_r); } break; 450 | case 5: { std::string _r = _t->getAlgorithmName(); 451 | if (_a[0]) *reinterpret_cast< std::string*>(_a[0]) = std::move(_r); } break; 452 | case 6: { std::vector _r = _t->getParameters(); 453 | if (_a[0]) *reinterpret_cast< std::vector*>(_a[0]) = std::move(_r); } break; 454 | case 7: { QWidget* _r = _t->getPluginUI(); 455 | if (_a[0]) *reinterpret_cast< QWidget**>(_a[0]) = std::move(_r); } break; 456 | case 8: _t->setImage((*reinterpret_cast< cv::Mat(*)>(_a[1])),(*reinterpret_cast< QString(*)>(_a[2]))); break; 457 | case 9: _t->setImage((*reinterpret_cast< cv::Mat(*)>(_a[1]))); break; 458 | case 10: _t->execute(); break; 459 | case 11: { std::vector _r = _t->getOutputImages(); 460 | if (_a[0]) *reinterpret_cast< std::vector*>(_a[0]) = std::move(_r); } break; 461 | case 12: { int _r = _t->getDisplayIndex(); 462 | if (_a[0]) *reinterpret_cast< int*>(_a[0]) = std::move(_r); } break; 463 | case 13: _t->setDisplayIndex((*reinterpret_cast< int(*)>(_a[1]))); break; 464 | case 14: { std::vector _r = _t->getFeatures(); 465 | if (_a[0]) *reinterpret_cast< std::vector*>(_a[0]) = std::move(_r); } break; 466 | case 15: { std::vector _r = _t->getFeatures((*reinterpret_cast< int(*)>(_a[1]))); 467 | if (_a[0]) *reinterpret_cast< std::vector*>(_a[0]) = std::move(_r); } break; 468 | case 16: _t->setBatchMode((*reinterpret_cast< bool(*)>(_a[1]))); break; 469 | case 17: { int _r = _t->saveOutput((*reinterpret_cast< QString(*)>(_a[1])),(*reinterpret_cast< QString(*)>(_a[2]))); 470 | if (_a[0]) *reinterpret_cast< int*>(_a[0]) = std::move(_r); } break; 471 | case 18: _t->saveMetadata((*reinterpret_cast< QString(*)>(_a[1])),(*reinterpret_cast< QString(*)>(_a[2])),(*reinterpret_cast< QString(*)>(_a[3]))); break; 472 | case 19: _t->saveMetadata((*reinterpret_cast< QString(*)>(_a[1])),(*reinterpret_cast< QString(*)>(_a[2]))); break; 473 | case 20: _t->loadMetadata((*reinterpret_cast< QString(*)>(_a[1]))); break; 474 | case 21: { int _r = _t->writeHeader((*reinterpret_cast< QString(*)>(_a[1])),(*reinterpret_cast< QString(*)>(_a[2]))); 475 | if (_a[0]) *reinterpret_cast< int*>(_a[0]) = std::move(_r); } break; 476 | case 22: { int _r = _t->writeHeader((*reinterpret_cast< QString(*)>(_a[1]))); 477 | if (_a[0]) *reinterpret_cast< int*>(_a[0]) = std::move(_r); } break; 478 | case 23: { std::vector _r = _t->getCSVColumnNames(); 479 | if (_a[0]) *reinterpret_cast< std::vector*>(_a[0]) = std::move(_r); } break; 480 | case 24: { int _r = _t->getProgressSteps(); 481 | if (_a[0]) *reinterpret_cast< int*>(_a[0]) = std::move(_r); } break; 482 | case 25: _t->abort(); break; 483 | case 26: { QChart* _r = _t->getChart(); 484 | if (_a[0]) *reinterpret_cast< QChart**>(_a[0]) = std::move(_r); } break; 485 | case 27: _t->updatesegmentedoutput(); break; 486 | default: ; 487 | } 488 | } else if (_c == QMetaObject::IndexOfMethod) { 489 | int *result = reinterpret_cast(_a[0]); 490 | { 491 | using _t = void (MainUI::*)(cv::Mat ); 492 | if (*reinterpret_cast<_t *>(_a[1]) == static_cast<_t>(&MainUI::updateVisualOutput)) { 493 | *result = 0; 494 | return; 495 | } 496 | } 497 | { 498 | using _t = void (MainUI::*)(QString ); 499 | if (*reinterpret_cast<_t *>(_a[1]) == static_cast<_t>(&MainUI::updateProgress)) { 500 | *result = 1; 501 | return; 502 | } 503 | } 504 | } 505 | } 506 | 507 | QT_INIT_METAOBJECT const QMetaObject MainUI::staticMetaObject = { { 508 | &QObject::staticMetaObject, 509 | qt_meta_stringdata_MainUI.data, 510 | qt_meta_data_MainUI, 511 | qt_static_metacall, 512 | nullptr, 513 | nullptr 514 | } }; 515 | 516 | 517 | const QMetaObject *MainUI::metaObject() const 518 | { 519 | return QObject::d_ptr->metaObject ? QObject::d_ptr->dynamicMetaObject() : &staticMetaObject; 520 | } 521 | 522 | void *MainUI::qt_metacast(const char *_clname) 523 | { 524 | if (!_clname) return nullptr; 525 | if (!strcmp(_clname, qt_meta_stringdata_MainUI.stringdata0)) 526 | return static_cast(this); 527 | if (!strcmp(_clname, "IPlugin")) 528 | return static_cast< IPlugin*>(this); 529 | if (!strcmp(_clname, "org.plugin.ImageProcessing.Segmentation.IPlugin")) 530 | return static_cast< IPlugin*>(this); 531 | return QObject::qt_metacast(_clname); 532 | } 533 | 534 | int MainUI::qt_metacall(QMetaObject::Call _c, int _id, void **_a) 535 | { 536 | _id = QObject::qt_metacall(_c, _id, _a); 537 | if (_id < 0) 538 | return _id; 539 | if (_c == QMetaObject::InvokeMetaMethod) { 540 | if (_id < 28) 541 | qt_static_metacall(this, _c, _id, _a); 542 | _id -= 28; 543 | } else if (_c == QMetaObject::RegisterMethodArgumentMetaType) { 544 | if (_id < 28) 545 | *reinterpret_cast(_a[0]) = -1; 546 | _id -= 28; 547 | } 548 | return _id; 549 | } 550 | 551 | // SIGNAL 0 552 | void MainUI::updateVisualOutput(cv::Mat _t1) 553 | { 554 | void *_a[] = { nullptr, const_cast(reinterpret_cast(&_t1)) }; 555 | QMetaObject::activate(this, &staticMetaObject, 0, _a); 556 | } 557 | 558 | // SIGNAL 1 559 | void MainUI::updateProgress(QString _t1) 560 | { 561 | void *_a[] = { nullptr, const_cast(reinterpret_cast(&_t1)) }; 562 | QMetaObject::activate(this, &staticMetaObject, 1, _a); 563 | } 564 | 565 | QT_PLUGIN_METADATA_SECTION 566 | static constexpr unsigned char qt_pluginMetaData[] = { 567 | 'Q', 'T', 'M', 'E', 'T', 'A', 'D', 'A', 'T', 'A', ' ', '!', 568 | // metadata version, Qt version, architectural requirements 569 | 0, QT_VERSION_MAJOR, QT_VERSION_MINOR, qPluginArchRequirements(), 570 | 0xbf, 571 | // "IID" 572 | 0x02, 0x78, 0x2f, 'o', 'r', 'g', '.', 'p', 573 | 'l', 'u', 'g', 'i', 'n', '.', 'I', 'm', 574 | 'a', 'g', 'e', 'P', 'r', 'o', 'c', 'e', 575 | 's', 's', 'i', 'n', 'g', '.', 'S', 'e', 576 | 'g', 'm', 'e', 'n', 't', 'a', 't', 'i', 577 | 'o', 'n', '.', 'I', 'P', 'l', 'u', 'g', 578 | 'i', 'n', 579 | // "className" 580 | 0x03, 0x66, 'M', 'a', 'i', 'n', 'U', 'I', 581 | 0xff, 582 | }; 583 | QT_MOC_EXPORT_PLUGIN(MainUI, MainUI) 584 | 585 | QT_WARNING_POP 586 | QT_END_MOC_NAMESPACE 587 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/resource.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/predictivephenomics/RhizoVisionExplorer/42750c9d238153dd2d707267c70dcbe66e302083/RhizoVisionExplorer/resource.h -------------------------------------------------------------------------------- /RhizoVisionExplorer/resources.qrc: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 10 | icons/rveicon.ico 11 | icons/RVElogoclearback-150.png 12 | icons/RVElogoclearback.png 13 | 14 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/rootsegmentprop.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (C) 2021, Anand Seethepalli and Larry York 3 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 4 | 5 | File: rootsegmentprop.cpp 6 | 7 | Authors: 8 | Anand Seethepalli (anand.seethepalli@yahoo.co.in) 9 | Larry York (larry.york@gmail.com) 10 | 11 | This file is part of RhizoVision Explorer. 12 | 13 | RhizoVision Explorer is free software: you can redistribute 14 | it and/or modify it under the terms of the GNU General Public 15 | License as published by the Free Software Foundation, either 16 | version 3 of the License, or (at your option) any later version. 17 | 18 | RhizoVision Explorer is distributed in the hope that it will 19 | be useful, but WITHOUT ANY WARRANTY; without even the implied 20 | warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 21 | PURPOSE. See the GNU General Public License for more details. 22 | 23 | You should have received a copy of the GNU General Public 24 | License along with RhizoVision Explorer; see the file COPYING. 25 | If not, see . 26 | */ 27 | 28 | // This file contains implementations of functions that extract 29 | // phenotypic traits from root segments such as total root length 30 | // as well as topological information such as first order and 31 | // second order roots, identification of main root, branching 32 | // frequency and average length before next branch. 33 | 34 | #include "roottopology.h" 35 | #include "rootsegmentprop.h" 36 | 37 | using namespace std; 38 | using namespace cv; 39 | 40 | void getrootlength(Mat skeleton, ListofListsRef segments, PointList overlap, double &rootlen) 41 | { 42 | rootlen = 0.0; 43 | Point diff; 44 | uchar *skel = skeleton.ptr(); 45 | double a = 0, b = 0; 46 | 47 | // Compute the sum of distances of root segments using 48 | // euclidean distance metric. 49 | for (int i = 0; i < segments.size(); i++) 50 | { 51 | for (int j = 0; j < segments[i].size() - 1; j++) 52 | { 53 | diff = segments[i][j] - segments[i][j + 1]; 54 | a = fabs(double(diff.x)); 55 | b = fabs(double(diff.y)); 56 | 57 | if (a == b) 58 | rootlen += a * CVUTIL_SQRT2; 59 | else if (a > b) 60 | rootlen += a; 61 | else 62 | rootlen += b; 63 | //rootlen += sqrt(diff.ddot(diff)); 64 | } 65 | } 66 | 67 | for (auto &overlappt : overlap) 68 | { 69 | // To check if the overlappt is a diagonal or orthogonal 70 | if (skel[overlappt.y * skeleton.cols + overlappt.x + 1] > 0) 71 | { 72 | // Orthogonal 73 | rootlen++; 74 | } 75 | else 76 | { 77 | // Diagonal 78 | rootlen += CVUTIL_SQRT2; 79 | //rootlen += sqrt(2); 80 | } 81 | } 82 | } 83 | 84 | //double getrootlength(Mat skeleton) 85 | //{ 86 | // double sum = 0.0; 87 | // Mat branchpt, endpt; 88 | // Points branchpts, endpts, overlap; 89 | // ListofLists segments; 90 | // 91 | // // Identify branch points and end points in the skeleton image. 92 | // getroottopology(skeleton, branchpts, endpts, overlap, segments); 93 | // 94 | // // Compute the sum of distances of root segments using 95 | // // euclidean distance metric. 96 | // getrootlength(skeleton, segments, overlap, sum); 97 | // 98 | // for (int i = 0; i < segments.size(); i++) 99 | // segments[i].resize(0); 100 | // 101 | // segments.resize(0); 102 | // overlap.resize(0); 103 | // endpts.resize(0); 104 | // branchpts.resize(0); 105 | // 106 | // return sum; 107 | //} 108 | 109 | void getrootradii(Mat skeleton, Mat segment, Mat dist, ListofListsRef segments, ListofListsRef radii, double& maxradius, int& maxradrowidx) 110 | { 111 | int i, j, x, y, xinc, yinc, currx, curry, nextx, nexty, nnextpt, ptcount; 112 | size_t cisz; 113 | 114 | Mat dskeleton; 115 | skeleton.convertTo(dskeleton, CV_64FC1); 116 | dskeleton = dskeleton / 255.0; 117 | 118 | Mat dt; 119 | dist.convertTo(dt, CV_64FC1); 120 | dt = dt.mul(dskeleton); 121 | double *dtptr = dt.ptr(); 122 | 123 | maxradius = -1.0; 124 | maxradrowidx = INT_MAX; 125 | 126 | // We now get the root radii at every skeletal pixel and for each segment. 127 | // Since, each segment contains points that describe the shape of the segment 128 | // in the simplest way possible, some pixels on the root segment may not be 129 | // present in the root segment. Hence, we traverse pixel-by-pixel in each 130 | // root segment and get list of radii for all the pixels for that root 131 | // segment. This lists of radii can further be used to perform statistics, 132 | // identify main root or even cluster the roots based on root radii. 133 | 134 | // First, to allocate sufficient memory. 135 | radii.resize(segments.size()); 136 | for (i = 0; i < segments.size(); i++) 137 | { 138 | cisz = segments[i].size() - 1; 139 | 140 | for (j = 0, ptcount = 0; j < cisz; j++) 141 | { 142 | nnextpt = j + 1; 143 | 144 | currx = segments[i][j].x; 145 | curry = segments[i][j].y; 146 | nextx = segments[i][nnextpt].x; 147 | nexty = segments[i][nnextpt].y; 148 | 149 | ptcount += max(abs(curry - nexty), abs(currx - nextx)); 150 | } 151 | 152 | radii[i].resize(ptcount + 1); 153 | } 154 | 155 | // Each root segment may start from a branch or an end point and 156 | // end at a branch or an end point. In case of an end point, the 157 | // radius is considered only once. But in case of branch point, 158 | // since it is connected to two other root segments, the radius 159 | // at the branch point is considered thrice in total. Hence, 160 | // when calculating average root radius across plant root, we need 161 | // to subtract twice the root radius at every branch point, to get 162 | // a better estimate. But, this function just makes list of root 163 | // radii of all the pixels that are present in each segment. 164 | for (i = 0; i < segments.size(); i++) 165 | { 166 | cisz = segments[i].size() - 1; 167 | ptcount = 0; 168 | 169 | for (j = 0; j < cisz; j++) 170 | { 171 | nnextpt = j + 1; 172 | 173 | currx = segments[i][j].x; 174 | curry = segments[i][j].y; 175 | nextx = segments[i][nnextpt].x; 176 | nexty = segments[i][nnextpt].y; 177 | 178 | if (nextx != currx) 179 | xinc = abs(currx - nextx) / (nextx - currx); 180 | else 181 | xinc = 0; 182 | 183 | if (nexty != curry) 184 | yinc = abs(curry - nexty) / (nexty - curry); 185 | else 186 | yinc = 0; 187 | 188 | for (x = currx, y = curry; !(x == nextx && y == nexty); x += xinc, y += yinc) 189 | { 190 | radii[i][ptcount++] = dtptr[y * dt.cols + x]; 191 | if (maxradius < dtptr[y * dt.cols + x]) 192 | { 193 | maxradius = dtptr[y * dt.cols + x]; 194 | maxradrowidx = y; 195 | } 196 | else if (maxradius == dtptr[y * dt.cols + x] && maxradrowidx > y) 197 | { 198 | maxradrowidx = y; 199 | } 200 | } 201 | } 202 | 203 | radii[i][ptcount] = dtptr[segments[i][j].y * dt.cols + segments[i][j].x]; 204 | 205 | if (maxradius < dtptr[segments[i][j].y * dt.cols + segments[i][j].x]) 206 | { 207 | maxradius = dtptr[segments[i][j].y * dt.cols + segments[i][j].x]; 208 | if (maxradrowidx > segments[i][j].y) 209 | maxradrowidx = segments[i][j].y; 210 | } 211 | } 212 | } 213 | 214 | void getrootradiiforsegments(ListofListsRef radii, ValueList avgradii) 215 | { 216 | double sum = 0.0; 217 | 218 | avgradii.resize(radii.size()); 219 | 220 | for (int i = 0; i < radii.size(); i++) 221 | { 222 | sum = 0.0; 223 | 224 | for (int j = 0; j < radii[i].size(); j++) 225 | sum += radii[i][j]; 226 | 227 | avgradii[i] = sum / radii[i].size(); 228 | } 229 | } 230 | 231 | void gethistogramofrootradii(Mat skeleton, Mat segment, ValueList x, IndexList y) 232 | { 233 | Mat dskeleton; 234 | int sum; 235 | 236 | skeleton.convertTo(dskeleton, CV_64FC1); 237 | dskeleton = dskeleton / 255.0; 238 | 239 | Mat dt = bwdist(segment); 240 | dt.convertTo(dt, CV_64FC1); 241 | dt = dt.mul(dskeleton); 242 | 243 | pair nonzeros = find(dt, FindType::IndicesAndValues); 244 | double *nzptr = nonzeros.second.ptr(); 245 | 246 | x = unique(nonzeros.second); 247 | int xsz = static_cast(x.size()); 248 | y.resize(xsz); 249 | 250 | for (int i = 0; i < xsz; i++) 251 | { 252 | sum = 0; 253 | for (int j = 0; j < nonzeros.second.rows; j++) 254 | if (x[i] == nzptr[j]) 255 | sum++; 256 | 257 | y[i] = sum; 258 | } 259 | } 260 | 261 | /// validatesegments () - Checks root segments for errors 262 | /// Validation rules: 263 | /// ---------------- 264 | /// 1. The internal points of root segments should not be shared with 265 | /// other root segments. 266 | /// 267 | /// 2. All the branch points should be used 3 times either as start points 268 | /// or end points by the root segments. 269 | /// 270 | /// 3. If a branch point is an overlapped point, it should be used 4 271 | /// times. All overlapped points must be used 4 times. 272 | /// 273 | /// 4. All end points must be used only once. 274 | /// 275 | /// 5. If an image is reconstructed with the root segments, it must 276 | /// form the complete skeleton. 277 | bool validatesegments(Mat skeleton, PointList branch, PointList end, PointList overlap, ListofListsRef rootsegments) 278 | { 279 | // The internal points of root segments should not be shared with 280 | // other root segments. 281 | size_t nsize = rootsegments.size(); 282 | 283 | vector sizesdata; 284 | sizesdata.resize(nsize); 285 | size_t *sizes = sizesdata.data(); 286 | 287 | for (size_t i = 0; i < rootsegments.size(); i++) 288 | sizes[i] = rootsegments[i].size(); 289 | 290 | for (int i = 0; i < nsize; i++) 291 | { 292 | //cout << "i = " << i << endl; 293 | 294 | for (int j = 1; j < (sizes[i] - 1); j++) 295 | { 296 | for (int k = i + 1; k < nsize; k++) 297 | { 298 | if (k == i) 299 | continue; 300 | 301 | for (int l = 1; l < (sizes[k] - 1); l++) 302 | { 303 | if (rootsegments[i][j].x == rootsegments[k][l].x && 304 | rootsegments[i][j].y == rootsegments[k][l].y) 305 | { 306 | #ifdef DEBUG_MESSAGES 307 | cout << "[" << __LINE__ << "]: x = " << rootsegments[i][j].x << " - y = " << rootsegments[i][j].y << endl; 308 | #endif 309 | return false; 310 | } 311 | } 312 | } 313 | } 314 | } 315 | 316 | /* All the branch points should be used 3 times either as start points 317 | or end points by the root segments. 318 | 319 | If a branch point is an overlapped point, it should be used 4 320 | times. All overlapped points must be used 4 times. 321 | 322 | All end points must be used only once. */ 323 | Dictionary bids, eids, oids; 324 | Point pt; 325 | bids.reserve(branch.size()); 326 | eids.reserve(end.size()); 327 | oids.reserve(overlap.size()); 328 | 329 | for (Point &p : branch) 330 | bids[p.x * 10000 + p.y] = -1; 331 | for (Point &p : end) 332 | eids[p.x * 10000 + p.y] = -1; 333 | for (Point &p : overlap) 334 | oids[p.x * 10000 + p.y] = -1; 335 | 336 | for (int i = 0; i < rootsegments.size(); i++) 337 | { 338 | pt = rootsegments[i][0]; 339 | 340 | if (bids[pt.x * 10000 + pt.y] != 0) 341 | { 342 | if (bids[pt.x * 10000 + pt.y] < 0) 343 | bids[pt.x * 10000 + pt.y] = 1; 344 | else 345 | bids[pt.x * 10000 + pt.y]++; 346 | } 347 | 348 | if (eids[pt.x * 10000 + pt.y] != 0) 349 | { 350 | if (eids[pt.x * 10000 + pt.y] < 0) 351 | eids[pt.x * 10000 + pt.y] = 1; 352 | else 353 | eids[pt.x * 10000 + pt.y]++; 354 | } 355 | 356 | if (oids[pt.x * 10000 + pt.y] != 0) 357 | { 358 | if (oids[pt.x * 10000 + pt.y] < 0) 359 | oids[pt.x * 10000 + pt.y] = 1; 360 | else 361 | oids[pt.x * 10000 + pt.y]++; 362 | } 363 | 364 | pt = rootsegments[i][rootsegments[i].size() - 1]; 365 | 366 | if (bids[pt.x * 10000 + pt.y] != 0) 367 | { 368 | if (bids[pt.x * 10000 + pt.y] < 0) 369 | bids[pt.x * 10000 + pt.y] = 1; 370 | else 371 | bids[pt.x * 10000 + pt.y]++; 372 | } 373 | 374 | if (eids[pt.x * 10000 + pt.y] != 0) 375 | { 376 | if (eids[pt.x * 10000 + pt.y] < 0) 377 | eids[pt.x * 10000 + pt.y] = 1; 378 | else 379 | eids[pt.x * 10000 + pt.y]++; 380 | } 381 | 382 | if (oids[pt.x * 10000 + pt.y] != 0) 383 | { 384 | if (oids[pt.x * 10000 + pt.y] < 0) 385 | oids[pt.x * 10000 + pt.y] = 1; 386 | else 387 | oids[pt.x * 10000 + pt.y]++; 388 | } 389 | } 390 | 391 | for (Point &p : branch) 392 | { 393 | if (bids[p.x * 10000 + p.y] != 3) 394 | { 395 | if (bids[p.x * 10000 + p.y] != 4 && bids[p.x * 10000 + p.y] != oids[p.x * 10000 + p.y]) 396 | { 397 | #ifdef DEBUG_MESSAGES 398 | cout << "[" << __LINE__ << "]: x = " << p.x << " - y = " << p.y << " bids = " << bids[p.x * 10000 + p.y] << " oids = " << oids[p.x * 10000 + p.y] << endl; 399 | //window("b1", skeleton.rowRange(p.y - 3, p.y + 4).colRange(p.x - 3, p.x + 4)); 400 | //window("b2", skeleton.rowRange(p.y - 103, p.y + 104).colRange(p.x - 103, p.x + 104)); 401 | #endif 402 | return false; 403 | } 404 | } 405 | } 406 | for (Point &p : end) 407 | { 408 | if (eids[p.x * 10000 + p.y] != 1) 409 | { 410 | #ifdef DEBUG_MESSAGES 411 | cout << "[" << __LINE__ << "]: x = " << p.x << " - y = " << p.y << endl; 412 | #endif 413 | return false; 414 | } 415 | } 416 | for (Point &p : overlap) 417 | { 418 | if (oids[p.x * 10000 + p.y] != 4) 419 | { 420 | #ifdef DEBUG_MESSAGES 421 | cout << "[" << __LINE__ << "]: x = " << p.x << " - y = " << p.y << endl; 422 | #endif 423 | return false; 424 | } 425 | } 426 | 427 | // If an image is reconstructed with the root segments, it must 428 | // form the complete skeleton. 429 | Mat rec = Mat::zeros(skeleton.size(), CV_8UC1); 430 | unsigned char *recptr = rec.ptr(); 431 | int currx, curry, nextx, nexty, xinc, yinc, x, y; 432 | const unsigned char white = static_cast(255); 433 | 434 | for (int i = 0; i < rootsegments.size(); i++) 435 | { 436 | for (int j = 0; j < rootsegments[i].size() - 1; j++) 437 | { 438 | currx = rootsegments[i][j].x - 1; 439 | curry = rootsegments[i][j].y - 1; 440 | nextx = rootsegments[i][j + 1].x - 1; 441 | nexty = rootsegments[i][j + 1].y - 1; 442 | 443 | if (!((currx == nextx) && (curry == nexty))) 444 | { 445 | if (currx == nextx) 446 | { 447 | yinc = abs(curry - nexty) / (nexty - curry); 448 | 449 | for (y = curry; y != nexty; y += yinc) 450 | recptr[y * rec.cols + currx] = white; 451 | } 452 | else if (curry == nexty) 453 | { 454 | xinc = abs(currx - nextx) / (nextx - currx); 455 | 456 | for (x = currx; x != nextx; x += xinc) 457 | recptr[curry * rec.cols + x] = white; 458 | } 459 | else 460 | { 461 | xinc = abs(currx - nextx) / (nextx - currx); 462 | yinc = abs(curry - nexty) / (nexty - curry); 463 | 464 | for (x = currx, y = curry; x != nextx; x += xinc, y += yinc) 465 | recptr[y * rec.cols + x] = white; 466 | } 467 | } 468 | 469 | recptr[nexty * rec.cols + nextx] = white; 470 | } 471 | } 472 | 473 | Mat diff = skeleton - rec; 474 | 475 | if (countNonZero(diff) > 0) 476 | { 477 | /*Mat mm; 478 | vector ch; 479 | 480 | ch.push_back(Mat::zeros(rec.size(), CV_8UC1)); 481 | ch.push_back(rec); 482 | ch.push_back(skeleton); 483 | 484 | merge(ch, mm); 485 | imwrite("C:\\Users\\aseethepalli\\Documents\\projects\\AltRhizo Lite\\working2\\bb.png", mm); 486 | window("b", mm.rowRange(5001 - 10, 5001 + 11).colRange(5250 - 10, 5250 + 11));*/ 487 | return false; 488 | } 489 | 490 | // We return true if all the conditions mentioned above are true. 491 | return true; 492 | } 493 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/rootsegmentprop.h: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (C) 2021, Anand Seethepalli and Larry York 3 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 4 | 5 | File: rootsegmentprop.h 6 | 7 | Authors: 8 | Anand Seethepalli (anand.seethepalli@yahoo.co.in) 9 | Larry York (larry.york@gmail.com) 10 | 11 | This file is part of RhizoVision Explorer. 12 | 13 | RhizoVision Explorer is free software: you can redistribute 14 | it and/or modify it under the terms of the GNU General Public 15 | License as published by the Free Software Foundation, either 16 | version 3 of the License, or (at your option) any later version. 17 | 18 | RhizoVision Explorer is distributed in the hope that it will 19 | be useful, but WITHOUT ANY WARRANTY; without even the implied 20 | warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 21 | PURPOSE. See the GNU General Public License for more details. 22 | 23 | You should have received a copy of the GNU General Public 24 | License along with RhizoVision Explorer; see the file COPYING. 25 | If not, see . 26 | */ 27 | 28 | #pragma once 29 | 30 | #ifndef ROOTSEGMENTPROP_H 31 | #define ROOTSEGMENTPROP_H 32 | 33 | #include "common_types.h" 34 | 35 | void getrootlength(cv::Mat skeleton, ListofListsRef segments, PointList overlap, double &rootlen); 36 | //double getrootlength(cv::Mat skeleton); 37 | 38 | void getrootradii(cv::Mat skeleton, cv::Mat segment, cv::Mat dist, ListofListsRef segments, ListofListsRef radii, double& maxradius, int& maxradrowidx); 39 | void getrootradiiforsegments(ListofListsRef radii, ValueList avgradii); 40 | 41 | void gethistogramofrootradii(cv::Mat skeleton, cv::Mat segment, ValueList x, IndexList y); 42 | 43 | bool validatesegments(cv::Mat skeleton, PointList branch, PointList end, PointList overlap, ListofListsRef rootsegments); 44 | 45 | #endif 46 | -------------------------------------------------------------------------------- /RhizoVisionExplorer/roottopology.h: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (C) 2021, Anand Seethepalli and Larry York 3 | Copyright (C) 2020, Courtesy of Noble Research Institute, LLC 4 | 5 | File: roottopology.h 6 | 7 | Authors: 8 | Anand Seethepalli (anand.seethepalli@yahoo.co.in) 9 | Larry York (larry.york@gmail.com) 10 | 11 | This file is part of RhizoVision Explorer. 12 | 13 | RhizoVision Explorer is free software: you can redistribute 14 | it and/or modify it under the terms of the GNU General Public 15 | License as published by the Free Software Foundation, either 16 | version 3 of the License, or (at your option) any later version. 17 | 18 | RhizoVision Explorer is distributed in the hope that it will 19 | be useful, but WITHOUT ANY WARRANTY; without even the implied 20 | warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 21 | PURPOSE. See the GNU General Public License for more details. 22 | 23 | You should have received a copy of the GNU General Public 24 | License along with RhizoVision Explorer; see the file COPYING. 25 | If not, see . 26 | */ 27 | 28 | #pragma once 29 | 30 | #ifndef ROOTTOPOLOGY_H 31 | #define ROOTTOPOLOGY_H 32 | 33 | #include "common_types.h" 34 | 35 | void getroottopology(cv::Mat &_skeleton, cv::Mat dist, PointList branchpts, PointList endpts, PointList overlappts, ListofListsRef rootsegments, bool pruneroots, int rootPruningThreshold); 36 | 37 | cv::Mat drawtopology(cv::Mat segmented, cv::Mat skeleton, PointList branchpts, PointList endpts, PointList overlappts); 38 | cv::Mat drawtopology2(cv::Mat segmented, cv::Scalar_ ranges, cv::Mat _skeleton, PointList branchpts, PointList endpts, PointList overlappts); 39 | 40 | cv::Mat drawtopology_wholeroot(cv::Mat img, cv::Scalar_ ranges, std::vector> cc, std::vector colorcodes, std::vector> colors); 41 | cv::Mat drawtopology_disconnectedroot(cv::Mat segmented, cv::Mat dist, cv::Scalar_ ranges, cv::Mat _skeleton, PointList branchpts, PointList endpts, PointList overlappts, int width); 42 | 43 | cv::Mat drawmedialaxis(cv::Mat dist, cv::Mat skel, std::vector rranges, int width); 44 | 45 | #endif 46 | 47 | -------------------------------------------------------------------------------- /changelog.txt: -------------------------------------------------------------------------------- 1 | version 2.0.3 2 | ------------- 3 | Source code updated to reflect transfer of copyright from Noble Research 4 | Institute, LLC to Anand Seethepalli and Larry York. 5 | 6 | Updated license to GNU GPL version 3. 7 | 8 | version 2.0.2 9 | ------------- 10 | New features: 11 | * The application is renamed to RhizoVision Explorer to reflect the huge revamp 12 | in the UI. The UI is expanded from only a batch processer for directories of 13 | images to a fully interactive tool. The application consists of a main window 14 | consisting of menus, toolbar and several panes such as analysis options, 15 | features, log, and ROI Manager. This functionality provided by cvutil library 16 | contains the following features. 17 | 1. Supports drag & drop of images to load. 18 | 2. Supports image panning and zooming. 19 | 3. Allows user to inspect pixel values in five different color spaces 20 | such as RGB, HSV, HLS, Lab and Luv. 21 | 4. Supports drawing Region-of-Interest (ROI) rectangles on the image 22 | to highlight important portions. 23 | 5. User can query pixel statistics of a loaded image in five different 24 | color spaces (mentioned above), either on an entire image, or the 25 | locations specified by ROIs. The statistics include mean and SD of 26 | the color channels. 27 | 6. The ROI subsystem supports selecting, moving, resizing and deleting 28 | multiple ROIs. Deleting the ROIs can be done using the delete key. 29 | Ctrl+A selects all the ROIs. All the ROIs can be deleted from the 30 | menu using Edit->ROI->Clear all ROIs. 31 | 7. The ROI subsystem also supports exporting and importing the ROIs as 32 | annotations in a text file. 33 | 8. The ROI Manager pane to the right of the main Window shows the ROIs 34 | that are currently present on the image. Selecting an ROI shows its 35 | dimensions, which can be edited in the pane. 36 | 9. The main window supports plugin system. When a plugin is loaded, its 37 | settings are populated to the left of the main window. Plugins are 38 | independent modules that implement a specific procedure/method/algorithm 39 | that can be attached to and configured frim inside the main window. 40 | 10. Main window supports browsing images in the same folder using left 41 | and right arrow keys. 42 | 11. Supports "Analyze" button in the toolbar, that invokes the current 43 | plugin loaded to perform analysis on the loaded image. 44 | 12. The main window has a log pane for logging info/warning/error messages 45 | and a features pane to display any extracted features from the plugin. 46 | Both the panes are located at the bottom of the main window. 47 | 13. The main window supports color inversion and 90 degree rotation of 48 | a loaded image. 49 | 14. If the current plugin has multiple outputs, these outputs can be 50 | browsed from the toolbar of the main window or by pressing SPACE key. 51 | SPACE key toggles the image displayed between input image and multiple 52 | output images. 53 | * The RhizoVision Explorer supports feature extraction from both root crown and 54 | broken root images that were acquired using flatbed scanner using Whole root 55 | and Brokwn root modes respectively. 56 | * The analysis options pane includes options for image pre-processing, feature 57 | extraction and output display. 58 | * The program can now convert pixels from mm using DPI value. 59 | * The program assumes the roots are darker and the background is brighter. 60 | Noise can be filtered by keeping largest connected component, filtering 61 | smaller dark components by size (non-roots) or filtering brighter components 62 | on dark components by size (fill roots). 63 | * Edge smoothing is now optional. 64 | * Feature extraction options include root pruning. Root pruning is a method 65 | where the lateral roots with root tips whose length is within the root diameter 66 | at the connecting branch plus the number of pixels given by the user. 67 | * Feature extraction options also include setting diameter ranges. A maximum 68 | of 10 ranges can be set. 69 | * User can configure how an output image can be displayed using output display 70 | options. This can be done using output display options. 71 | * After analysis the relevant features from either whole root or broken roots 72 | are extracted and populated in the Features pane at the bottom of the main 73 | window. 74 | * A histogram pane shows after running analysis that shows the total length in 75 | each diameter bin and updates with new analysis 76 | * Help has an About dialog with information about the version, license, and 77 | contact information. 78 | * The program now extracts histograms of root length, projected area, surface 79 | area and volume with bins as the diameter ranges given by the user in the 80 | Analysis options pane. 81 | * While extracting features of an image in interactive mode, a prograss bar 82 | shows the amount of progress and the steps currently running on the image. 83 | * If the images are taken in a different rotation, they can be rotated and 84 | analyzed within the program. 85 | * If Region-of-Interests (ROIs) are drawn on an image, the program only analyzes 86 | the image data in the ROIs. This may be helpful, when cropping borders or 87 | if an image has multiple root samples that require separate processing. 88 | The batch analysis also applies the existing ROIs to every image in the 89 | folder before analyzing. 90 | * The program now supports root pruning. Enabling the pruning option with 91 | a threshold level discards root segments greater than the radius of the 92 | parent segment plus the threshold level. 93 | 94 | Fixes: 95 | * main.cpp: Fixed type casting variables from unsigned int to signed int. 96 | * MainUI.cpp: Fixed loading/saving image paths to use QFile instead of fstream 97 | to fix errors when the path has non-English characters. 98 | 99 | Version 1.0: 100 | ----------- 101 | New features: 102 | ------------ 103 | * Modified feature extraction function to extract features in two separate threads. 104 | * Calculated area of convex polygon without drawing the pixels in a separate image. 105 | * Added About dialog box. 106 | * Added in-program documentation. It can be accessed by clicking '?' symbol at the 107 | top right corner and clicking the user interface controls. 108 | * Added support for file types: PNG, JPG, BMP, JPEG, JPE, DIB, JP2, TIFF, TIF. 109 | * The program now saves the user options in a separate metadata.csv in the same 110 | output folder along with features.csv for future reference. 111 | * Added icons and logo to the software. 112 | 113 | Issues fixed: 114 | ------------ 115 | * Replaced conventional rand() function from C to random_device in C++ for longer 116 | periodicity. 117 | * Fixed program to crop empty regions before performing analysis to improve speed. 118 | * Before extracting median and maximum root numbers, the program now skips zeros 119 | from the list of root numbers from each rows. 120 | * Fixed estimation of Perimeter, where the program computed the sum of distances 121 | between contour points excluding the segment that connects first and last contour 122 | points in a circular contour. 123 | * Average and median diameter is now zero for an empty image where the program 124 | previously crashed for the input. 125 | * Fixed estimation of volume and surface area of plant root so that the extracted 126 | feature is invariant to rotation of image. This issue was observed when an image 127 | was created containing manually drawn straight line of same length but at different 128 | angles was passed to RhizoVision Analyzer. 129 | * The program now saves root diameters (average, median and maximum) instead of 130 | radii for easier verification by end users. 131 | * Fixed generation of orientation histograms as the program iterates only a few 132 | points due to wrong loop condition. 133 | * Fixed generation of orientation histograms where the program crashed when the 134 | root segment has only one pixel. 135 | * The program is fixed to check the availability of Intel AVX 2.0 instruction set 136 | and enable vector acceleration accordingly. 137 | * Fixed estimation of maximum diameter to scan all skeletal pixels and select the 138 | location of the pixel having maximum diameter that has highest row index (or 139 | greatest depth). 140 | 141 | Version 0.91 142 | ------------ 143 | New features: 144 | ------------ 145 | * Added UI option to save binary segmented images. 146 | * Added two new features - Number of Root Tips and Average Root Angle. 147 | * Added UI controls to set diameter ranges. 148 | * Added UI controls to manually set the threshold level. 149 | 150 | Issues fixed: 151 | ------------ 152 | * Fixed issues where ghost skeletons are created. 153 | * Fixed issue in skeletonization where the ridges were not connected to the main ridge 154 | due to mis-identification of ridge endpoints. 155 | * The distanceTransform() on OpenCV returns wrong distances (for precise Euclidean 156 | distances) for pixels with location greater than 4096 rows or columns. This may 157 | make harder to compute distance transforms for larger sized images. Although 158 | OpenCV is open-source, it internally calls functions from Intel's proprietary 159 | library called Intel Performance Premitives (IPP) to compute the precise Euclidean 160 | distance transforms. Currently implemented the same algorithm as referred in IPP 161 | manually. 162 | 163 | Version 0.9 164 | ----------- 165 | New features: 166 | ------------ 167 | * The program is converted to a GUI. The feature extraction runs on a separate thread, 168 | while progress is shown on main window. 169 | * The user can specify in the window, the location of the images to be processed and 170 | the output location. 171 | * The program can optionally output processed images. 172 | * The program can optionally convert features from pixel units to physical units (millimeters). 173 | * An additional feature 'Average Hole Size' is extracted from the plant root images. 174 | 175 | Issues fixed: 176 | ------------ 177 | * demo.h:getnearestcomponents() - Fixed an issue where nearest components were wrongly 178 | assigned. 179 | * main.cpp:getcoarsefineroots() - The coarse, medium and fine roots are returned as 180 | fraction of the total number of roots. 181 | * main.cpp:getshallowdeeproots() - The shallow, medium and deep roots are returned as 182 | fraction of the total number of roots. 183 | * main.cpp:feature_extractor() - Fixed the function to convert features from pixel units 184 | to physical units (millimeters). 185 | * roottopology.cpp:getroottolopogy() - Fixed a memory leak issue, that leads to large 186 | memory allocation of the order of 9 GB when the program is run on 4000 images. 187 | 188 | Version 0.1 189 | ----------- 190 | * Initial creation. 191 | * The program runs in console window and extracts plant root features from each image in a specified directory. 192 | --------------------------------------------------------------------------------