1 | /* |
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2 | * ---------------------------------------------------------------------- |
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3 | * RpDicomToVtk - |
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4 | * |
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5 | * ====================================================================== |
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6 | * AUTHOR: Leif Delgass, Purdue University |
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7 | * Copyright (c) 2014 HUBzero Foundation, LLC |
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8 | * |
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9 | * See the file "license.terms" for information on usage and |
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10 | * redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES. |
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11 | * ====================================================================== |
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12 | */ |
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13 | |
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14 | #include <vtkSmartPointer.h> |
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15 | #include <vtkStringArray.h> |
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16 | #include <vtkIntArray.h> |
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17 | #include <vtkDataSetWriter.h> |
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18 | #include <vtkDirectory.h> |
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19 | #ifdef USE_VTK_DICOM_PACKAGE |
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20 | #include <vtkDICOMSorter.h> |
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21 | #include <vtkDICOMReader.h> |
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22 | #include <vtkDICOMMetaData.h> |
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23 | #else |
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24 | #include <vtkDICOMImageReader.h> |
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25 | #endif |
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26 | |
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27 | #include <stdio.h> |
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28 | #include "tcl.h" |
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29 | |
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30 | static int |
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31 | DicomToVtkCmd(ClientData clientData, Tcl_Interp *interp, int objc, |
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32 | Tcl_Obj *const *objv) |
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33 | { |
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34 | if (objc != 3) { |
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35 | Tcl_AppendResult(interp, "wrong # args: should be \"", |
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36 | Tcl_GetString(objv[0]), " dir|files fileList\"", (char*)NULL); |
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37 | return TCL_ERROR; |
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38 | } |
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39 | bool isDir = false; |
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40 | char *arg = Tcl_GetString(objv[1]); |
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41 | if (arg[0] == 'd' && strcmp(arg, "dir") == 0) { |
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42 | isDir = true; |
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43 | } |
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44 | |
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45 | char *dirName = NULL; |
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46 | vtkSmartPointer<vtkStringArray> pathArray = vtkSmartPointer<vtkStringArray>::New(); |
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47 | if (isDir) { |
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48 | dirName = Tcl_GetString(objv[2]); |
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49 | } else { |
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50 | // Get path array from Tcl list |
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51 | int pathListc; |
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52 | Tcl_Obj **pathListv = NULL; |
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53 | if (Tcl_ListObjGetElements(interp, objv[2], &pathListc, &pathListv) != TCL_OK) { |
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54 | return TCL_ERROR; |
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55 | } |
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56 | pathArray->SetNumberOfValues(pathListc); |
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57 | for (int i = 0; i < pathListc; i++) { |
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58 | pathArray->SetValue(i, Tcl_GetString(pathListv[i])); |
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59 | } |
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60 | } |
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61 | |
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62 | #ifdef USE_VTK_DICOM_PACKAGE |
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63 | vtkSmartPointer<vtkDICOMReader> reader = vtkSmartPointer<vtkDICOMReader>::New(); |
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64 | vtkSmartPointer<vtkDICOMSorter> sorter = vtkSmartPointer<vtkDICOMSorter>::New(); |
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65 | if (isDir) { |
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66 | vtkSmartPointer<vtkDirectory> dir = vtkSmartPointer<vtkDirectory>::New(); |
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67 | if (!dir->Open(dirName)) { |
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68 | return TCL_ERROR; |
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69 | } |
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70 | |
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71 | int numFiles = dir->GetNumberOfFiles(); |
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72 | for (int i = 0; i < numFiles; i++) { |
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73 | if (dir->GetFile(i)[0] == '.') { |
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74 | continue; |
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75 | } |
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76 | |
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77 | std::string path(dirName); |
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78 | path += "/"; |
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79 | path += dir->GetFile(i); |
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80 | |
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81 | if (!dir->FileIsDirectory(path.c_str()) && |
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82 | reader->CanReadFile(path.c_str())) { |
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83 | pathArray->InsertNextValue(path); |
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84 | } else { |
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85 | fprintf(stderr, "Skipping file %s\n", path.c_str()); |
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86 | } |
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87 | } |
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88 | } |
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89 | |
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90 | sorter->SetInputFileNames(pathArray); |
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91 | sorter->Update(); |
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92 | |
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93 | int numStudies = sorter->GetNumberOfStudies(); |
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94 | int study = 0; |
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95 | int series = 0; |
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96 | |
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97 | fprintf(stderr, "Num Studies: %d\n", numStudies); |
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98 | vtkStringArray *files; |
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99 | #if 0 |
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100 | for (int i = 0; i < numStudies; i++) { |
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101 | int numSeries = sorter->GetNumberOfSeriesInStudy(i); |
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102 | fprintf(stderr, "Study %d: %d series\n", i, numSeries); |
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103 | int k = sorter->GetFirstSeriesInStudy(i); |
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104 | for (int j = 0; j < numSeries; j++) { |
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105 | files = sorter->GetFileNamesForSeries(k+j); |
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106 | } |
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107 | } |
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108 | #else |
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109 | if (study < 0 || study > sorter->GetNumberOfStudies()-1) { |
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110 | return TCL_ERROR; |
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111 | } |
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112 | if (series < 0 || series > sorter->GetNumberOfSeriesInStudy(study)-1) { |
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113 | return TCL_ERROR; |
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114 | } |
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115 | files = sorter->GetFileNamesForSeries(sorter->GetFirstSeriesInStudy(study)+series); |
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116 | #endif |
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117 | |
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118 | Tcl_Obj *objPtr = Tcl_NewListObj(0, NULL); |
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119 | Tcl_Obj *metaDataObj = Tcl_NewListObj(0, NULL); |
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120 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_studies", -1)); |
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121 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(numStudies)); |
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122 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study", -1)); |
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123 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(study)); |
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124 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_series", -1)); |
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125 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(sorter->GetNumberOfSeriesInStudy(study))); |
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126 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series", -1)); |
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127 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(series)); |
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128 | |
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129 | reader->SetFileNames(files); |
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130 | #else |
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131 | Tcl_Obj *objPtr = Tcl_NewListObj(0, NULL); |
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132 | Tcl_Obj *metaDataObj = Tcl_NewListObj(0, NULL); |
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133 | |
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134 | vtkSmartPointer<vtkDICOMImageReader> reader = vtkSmartPointer<vtkDICOMImageReader>::New(); |
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135 | if (isDir) { |
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136 | reader->SetDirectoryName(dirName); |
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137 | } else { |
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138 | reader->SetFileName(pathArray->GetValue(0)); |
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139 | } |
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140 | #endif |
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141 | reader->Update(); |
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142 | |
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143 | Tcl_Obj *eltObj; |
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144 | #ifdef USE_VTK_DICOM_PACKAGE |
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145 | vtkStringArray *ids = reader->GetStackIDs(); |
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146 | for (int i = 0; i < ids->GetNumberOfValues(); i++) { |
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147 | fprintf(stderr, "Stack: %s\n", ids->GetValue(i).c_str()); |
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148 | } |
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149 | vtkIntArray *fidxArray = reader->GetFileIndexArray(); |
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150 | vtkDICOMMetaData *md = reader->GetMetaData(); |
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151 | int numComp = fidxArray->GetNumberOfComponents(); |
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152 | #if 0 |
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153 | for (int i = 0; i < fidxArray->GetNumberOfTuples(); i++) { |
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154 | fprintf(stderr, "%d:", i); |
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155 | for (int j = 0; j < fidxArray->GetNumberOfComponents(); j++) { |
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156 | int idx = (int)fidxArray->GetComponent(i, j); |
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157 | fprintf(stderr, " %d", idx); |
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158 | } |
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159 | fprintf(stderr, "\n"); |
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160 | } |
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161 | #endif |
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162 | fprintf(stderr, "Number of data elements: %d\n", md->GetNumberOfDataElements()); |
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163 | |
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164 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_files", -1)); |
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165 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetNumberOfInstances())); |
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166 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_components", -1)); |
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167 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(numComp)); |
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168 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("modality", -1)); |
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169 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::Modality).AsString().c_str(), -1)); |
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170 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("patient_name", -1)); |
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171 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::PatientName).AsString().c_str(), -1)); |
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172 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("transfer_syntax_uid", -1)); |
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173 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::TransferSyntaxUID).AsString().c_str(), -1)); |
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174 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_uid", -1)); |
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175 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::StudyInstanceUID).AsString().c_str(), -1)); |
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176 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_id", -1)); |
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177 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::StudyID).AsString().c_str(), -1)); |
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178 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series_number", -1)); |
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179 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::SeriesNumber).AsInt())); |
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180 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series_in_study", -1)); |
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181 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::SeriesInStudy).AsInt())); |
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182 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series_uid", -1)); |
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183 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::SeriesInstanceUID).AsString().c_str(), -1)); |
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184 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("bits_allocated", -1)); |
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185 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::BitsAllocated).AsInt())); |
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186 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("bits_stored", -1)); |
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187 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::BitsStored).AsInt())); |
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188 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("pixel_representation", -1)); |
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189 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::PixelRepresentation).AsString().c_str(), -1)); |
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190 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_slope", -1)); |
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191 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(md->GetAttributeValue(DC::RescaleSlope).AsDouble())); |
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192 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_intercept", -1)); |
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193 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(md->GetAttributeValue(DC::RescaleIntercept).AsDouble())); |
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194 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("time_dimension", -1)); |
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195 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(reader->GetTimeDimension())); |
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196 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("time_spacing", -1)); |
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197 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetTimeSpacing())); |
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198 | #else |
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199 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("patient_name", -1)); |
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200 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetPatientName(), -1)); |
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201 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("transfer_syntax_uid", -1)); |
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202 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetTransferSyntaxUID(), -1)); |
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203 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_uid", -1)); |
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204 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetStudyUID(), -1)); |
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205 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_id", -1)); |
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206 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetStudyID(), -1)); |
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207 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_components", -1)); |
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208 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(reader->GetNumberOfComponents())); |
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209 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("bits_allocated", -1)); |
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210 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(reader->GetBitsAllocated())); |
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211 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("pixel_representation", -1)); |
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212 | Tcl_ListObjAppendElement(interp, metaDataObj, |
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213 | Tcl_NewStringObj((reader->GetPixelRepresentation() ? "signed" : "unsigned"), -1)); |
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214 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_slope", -1)); |
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215 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetRescaleSlope())); |
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216 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_offset", -1)); |
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217 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetRescaleOffset())); |
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218 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("gantry_angle", -1)); |
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219 | Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetGantryAngle())); |
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220 | #if 0 |
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221 | fprintf(stderr, "Position: %g %g %g\n", |
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222 | reader->GetImagePositionPatient()[0], |
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223 | reader->GetImagePositionPatient()[1], |
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224 | reader->GetImagePositionPatient()[2]); |
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225 | fprintf(stderr, "Orientation: %g %g %g, %g %g %g\n", |
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226 | reader->GetImageOrientationPatient()[0], |
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227 | reader->GetImageOrientationPatient()[1], |
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228 | reader->GetImageOrientationPatient()[2], |
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229 | reader->GetImageOrientationPatient()[3], |
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230 | reader->GetImageOrientationPatient()[4], |
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231 | reader->GetImageOrientationPatient()[5]); |
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232 | #endif |
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233 | #endif |
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234 | |
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235 | Tcl_ListObjAppendList(interp, objPtr, metaDataObj); |
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236 | |
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237 | fprintf(stderr, "writing VTK\n"); |
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238 | |
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239 | vtkSmartPointer<vtkDataSetWriter> writer = vtkSmartPointer<vtkDataSetWriter>::New(); |
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240 | writer->SetInputConnection(reader->GetOutputPort()); |
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241 | writer->SetFileTypeToBinary(); |
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242 | writer->WriteToOutputStringOn(); |
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243 | writer->Update(); |
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244 | |
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245 | fprintf(stderr, "writing VTK...done\n"); |
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246 | |
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247 | Tcl_ListObjAppendElement(interp, objPtr, Tcl_NewStringObj("vtkdata", -1)); |
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248 | |
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249 | eltObj = Tcl_NewByteArrayObj((unsigned char *)writer->GetBinaryOutputString(), |
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250 | writer->GetOutputStringLength()); |
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251 | Tcl_ListObjAppendElement(interp, objPtr, eltObj); |
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252 | |
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253 | Tcl_SetObjResult(interp, objPtr); |
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254 | return TCL_OK; |
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255 | } |
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256 | |
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257 | extern "C" { |
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258 | /* |
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259 | * ------------------------------------------------------------------------ |
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260 | * RpDicomToVtk_Init -- |
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261 | * |
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262 | * Invoked when the Rappture GUI library is being initialized |
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263 | * to install the "DicomToVtk" command into the interpreter. |
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264 | * |
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265 | * Returns TCL_OK if successful, or TCL_ERROR (along with an error |
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266 | * message in the interp) if anything goes wrong. |
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267 | * ------------------------------------------------------------------------ |
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268 | */ |
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269 | int |
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270 | RpDicomToVtk_Init(Tcl_Interp *interp) |
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271 | { |
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272 | /* install the widget command */ |
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273 | Tcl_CreateObjCommand(interp, "Rappture::DicomToVtk", DicomToVtkCmd, |
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274 | NULL, NULL); |
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275 | return TCL_OK; |
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276 | } |
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277 | |
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278 | } |
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