source: branches/uq/gui/src/RpDicomToVtk.cc @ 5121

Last change on this file since 5121 was 5121, checked in by dkearney, 10 years ago

merging updates from 1.3 branch

looks like this branch originally came from the 1.3 branch and then had some
additions from the 1.4-pre branch and then a sync from the 1.3 branch. to get
this branch updated, I am reverting r4797 (additions from 1.4-pre branch),
reverting r4798 (additions from 1.3 branch), then merging in updates from 1.3
branch.

I fixed merge conflicts for the following files:

gui/scripts/gauge.tcl
gui/scripts/main.tcl
gui/scripts/tool.tcl
lang/tcl/scripts/task.tcl
File size: 13.0 KB
Line 
1/*
2 * ----------------------------------------------------------------------
3 *  RpDicomToVtk -
4 *
5 * ======================================================================
6 *  AUTHOR:  Leif Delgass, Purdue University
7 *  Copyright (c) 2014  HUBzero Foundation, LLC
8 *
9 *  See the file "license.terms" for information on usage and
10 *  redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES.
11 * ======================================================================
12 */
13
14#include <vtkSmartPointer.h>
15#include <vtkStringArray.h>
16#include <vtkIntArray.h>
17#include <vtkDataSetWriter.h>
18#include <vtkDirectory.h>
19#ifdef USE_VTK_DICOM_PACKAGE
20#include <vtkDICOMSorter.h>
21#include <vtkDICOMReader.h>
22#include <vtkDICOMMetaData.h>
23#else
24#include <vtkDICOMImageReader.h>
25#endif
26
27#include <stdio.h>
28#include "tcl.h"
29
30// #define RP_DICOM_TRACE
31
32static int
33DicomToVtkCmd(ClientData clientData, Tcl_Interp *interp, int objc,
34              Tcl_Obj *const *objv)
35{
36    if (objc != 3) {
37        Tcl_AppendResult(interp, "wrong # args: should be \"",
38                         Tcl_GetString(objv[0]), " dir|files fileList\"", (char*)NULL);
39        return TCL_ERROR;
40    }
41    bool isDir = false;
42    char *arg = Tcl_GetString(objv[1]);
43    if (arg[0] == 'd' && strcmp(arg, "dir") == 0) {
44        isDir = true;
45    }
46
47    char *dirName = NULL;
48    vtkSmartPointer<vtkStringArray> pathArray = vtkSmartPointer<vtkStringArray>::New();
49    if (isDir) {
50        dirName = Tcl_GetString(objv[2]);
51    } else {
52        // Get path array from Tcl list
53        int pathListc;
54        Tcl_Obj **pathListv = NULL;
55        if (Tcl_ListObjGetElements(interp, objv[2], &pathListc, &pathListv) != TCL_OK) {
56            return TCL_ERROR;
57        }
58        pathArray->SetNumberOfValues(pathListc);
59        for (int i = 0; i < pathListc; i++) {
60            pathArray->SetValue(i, Tcl_GetString(pathListv[i]));
61        }
62    }
63
64#ifdef USE_VTK_DICOM_PACKAGE
65    vtkSmartPointer<vtkDICOMReader> reader = vtkSmartPointer<vtkDICOMReader>::New();
66    vtkSmartPointer<vtkDICOMSorter> sorter = vtkSmartPointer<vtkDICOMSorter>::New();
67    if (isDir) {
68        vtkSmartPointer<vtkDirectory> dir = vtkSmartPointer<vtkDirectory>::New();
69        if (!dir->Open(dirName)) {
70            return TCL_ERROR;
71        }
72
73        int numFiles = dir->GetNumberOfFiles();
74        for (int i = 0; i < numFiles; i++) {
75            if (dir->GetFile(i)[0] == '.') {
76                continue;
77            }
78
79            std::string path(dirName);
80            path += "/";
81            path += dir->GetFile(i);
82
83            if (!dir->FileIsDirectory(path.c_str()) &&
84                reader->CanReadFile(path.c_str())) {
85                pathArray->InsertNextValue(path);
86            } else {
87                fprintf(stderr, "Skipping file %s\n", path.c_str());
88            }
89        }
90    }
91
92    sorter->SetInputFileNames(pathArray);
93    sorter->Update();
94
95    int numStudies = sorter->GetNumberOfStudies();
96    int study = 0;
97    int series = 0;
98
99#ifdef RP_DICOM_TRACE
100    fprintf(stderr, "Num Studies: %d\n", numStudies);
101#endif
102    vtkStringArray *files;
103#if 0
104    for (int i = 0; i < numStudies; i++) {
105        int numSeries = sorter->GetNumberOfSeriesInStudy(i);
106#ifdef RP_DICOM_TRACE
107        fprintf(stderr, "Study %d: %d series\n", i, numSeries);
108#endif
109        int k = sorter->GetFirstSeriesInStudy(i);
110        for (int j = 0; j < numSeries; j++) {
111            files = sorter->GetFileNamesForSeries(k+j);
112        }
113    }
114#else
115    if (study < 0 || study > sorter->GetNumberOfStudies()-1) {
116        return TCL_ERROR;
117    }
118    if (series < 0 || series > sorter->GetNumberOfSeriesInStudy(study)-1) {
119        return TCL_ERROR;
120    }
121    files = sorter->GetFileNamesForSeries(sorter->GetFirstSeriesInStudy(study)+series);
122#endif
123
124    Tcl_Obj *objPtr = Tcl_NewListObj(0, NULL);
125    Tcl_Obj *metaDataObj = Tcl_NewListObj(0, NULL);
126    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_studies", -1));
127    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(numStudies));
128    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study", -1));
129    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(study));
130    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_series", -1));
131    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(sorter->GetNumberOfSeriesInStudy(study)));
132    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series", -1));
133    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(series));
134
135    reader->SetFileNames(files);
136#else
137    Tcl_Obj *objPtr = Tcl_NewListObj(0, NULL);
138    Tcl_Obj *metaDataObj = Tcl_NewListObj(0, NULL);
139
140    vtkSmartPointer<vtkDICOMImageReader> reader = vtkSmartPointer<vtkDICOMImageReader>::New();
141    if (isDir) {
142        reader->SetDirectoryName(dirName);
143    } else {
144        reader->SetFileName(pathArray->GetValue(0));
145    }
146#endif
147    reader->Update();
148
149    Tcl_Obj *eltObj;
150#ifdef USE_VTK_DICOM_PACKAGE
151    vtkStringArray *ids = reader->GetStackIDs();
152#ifdef RP_DICOM_TRACE
153    for (int i = 0; i < ids->GetNumberOfValues(); i++) {
154        fprintf(stderr, "Stack: %s\n", ids->GetValue(i).c_str());
155    }
156#endif
157    vtkIntArray *fidxArray = reader->GetFileIndexArray();
158    vtkDICOMMetaData *md = reader->GetMetaData();
159    int numComp = fidxArray->GetNumberOfComponents();
160#if 0
161    for (int i = 0; i < fidxArray->GetNumberOfTuples(); i++) {
162        fprintf(stderr, "%d:", i);
163        for (int j = 0; j < fidxArray->GetNumberOfComponents(); j++) {
164            int idx = (int)fidxArray->GetComponent(i, j);
165            fprintf(stderr, " %d", idx);
166        }
167        fprintf(stderr, "\n");
168    }
169#endif
170#ifdef RP_DICOM_TRACE
171    fprintf(stderr, "Number of data elements: %d\n", md->GetNumberOfDataElements());
172#endif
173    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_files", -1));
174    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetNumberOfInstances()));
175    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_components", -1));
176    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(numComp));
177    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("modality", -1));
178    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::Modality).AsString().c_str(), -1));
179    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("patient_name", -1));
180    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::PatientName).AsString().c_str(), -1));
181    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("transfer_syntax_uid", -1));
182    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::TransferSyntaxUID).AsString().c_str(), -1));
183    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_uid", -1));
184    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::StudyInstanceUID).AsString().c_str(), -1));
185    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_id", -1));
186    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::StudyID).AsString().c_str(), -1));
187    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series_number", -1));
188    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::SeriesNumber).AsInt()));
189    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series_in_study", -1));
190    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::SeriesInStudy).AsInt()));
191    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("series_uid", -1));
192    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::SeriesInstanceUID).AsString().c_str(), -1));
193    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("bits_allocated", -1));
194    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::BitsAllocated).AsInt()));
195    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("bits_stored", -1));
196    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(md->GetAttributeValue(DC::BitsStored).AsInt()));
197    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("pixel_representation", -1));
198    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(md->GetAttributeValue(DC::PixelRepresentation).AsString().c_str(), -1));
199    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_slope", -1));
200    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(md->GetAttributeValue(DC::RescaleSlope).AsDouble()));
201    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_intercept", -1));
202    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(md->GetAttributeValue(DC::RescaleIntercept).AsDouble()));
203    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("time_dimension", -1));
204    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(reader->GetTimeDimension()));
205    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("time_spacing", -1));
206    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetTimeSpacing()));
207#else
208    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("patient_name", -1));
209    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetPatientName(), -1));
210    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("transfer_syntax_uid", -1));
211    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetTransferSyntaxUID(), -1));
212    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_uid", -1));
213    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetStudyUID(), -1));
214    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("study_id", -1));
215    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj(reader->GetStudyID(), -1));
216    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("num_components", -1));
217    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(reader->GetNumberOfComponents()));
218    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("bits_allocated", -1));
219    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewIntObj(reader->GetBitsAllocated()));
220    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("pixel_representation", -1));
221    Tcl_ListObjAppendElement(interp, metaDataObj,
222                             Tcl_NewStringObj((reader->GetPixelRepresentation() ? "signed" : "unsigned"), -1));
223    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_slope", -1));
224    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetRescaleSlope()));
225    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("rescale_offset", -1));
226    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetRescaleOffset()));
227    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewStringObj("gantry_angle", -1));
228    Tcl_ListObjAppendElement(interp, metaDataObj, Tcl_NewDoubleObj(reader->GetGantryAngle()));
229#if 0
230    fprintf(stderr, "Position: %g %g %g\n",
231            reader->GetImagePositionPatient()[0],
232            reader->GetImagePositionPatient()[1],
233            reader->GetImagePositionPatient()[2]);
234    fprintf(stderr, "Orientation: %g %g %g, %g %g %g\n",
235            reader->GetImageOrientationPatient()[0],
236            reader->GetImageOrientationPatient()[1],
237            reader->GetImageOrientationPatient()[2],
238            reader->GetImageOrientationPatient()[3],
239            reader->GetImageOrientationPatient()[4],
240            reader->GetImageOrientationPatient()[5]);
241#endif
242#endif
243
244    Tcl_ListObjAppendList(interp, objPtr, metaDataObj);
245#ifdef RP_DICOM_TRACE
246    fprintf(stderr, "writing VTK\n");
247#endif
248    vtkSmartPointer<vtkDataSetWriter> writer = vtkSmartPointer<vtkDataSetWriter>::New();
249    writer->SetInputConnection(reader->GetOutputPort());
250    writer->SetFileTypeToBinary();
251    writer->WriteToOutputStringOn();
252    writer->Update();
253#ifdef RP_DICOM_TRACE
254    fprintf(stderr, "writing VTK...done\n");
255#endif
256    Tcl_ListObjAppendElement(interp, objPtr, Tcl_NewStringObj("vtkdata", -1));
257
258    eltObj = Tcl_NewByteArrayObj((unsigned char *)writer->GetBinaryOutputString(),
259                                 writer->GetOutputStringLength());
260    Tcl_ListObjAppendElement(interp, objPtr, eltObj);
261
262    Tcl_SetObjResult(interp, objPtr);
263    return TCL_OK;
264}
265
266extern "C" {
267/*
268 * ------------------------------------------------------------------------
269 *  RpDicomToVtk_Init --
270 *
271 *  Invoked when the Rappture GUI library is being initialized
272 *  to install the "DicomToVtk" command into the interpreter.
273 *
274 *  Returns TCL_OK if successful, or TCL_ERROR (along with an error
275 *  message in the interp) if anything goes wrong.
276 * ------------------------------------------------------------------------
277 */
278int
279RpDicomToVtk_Init(Tcl_Interp *interp)
280{
281    /* install the widget command */
282    Tcl_CreateObjCommand(interp, "Rappture::DicomToVtk", DicomToVtkCmd,
283                         NULL, NULL);
284    return TCL_OK;
285}
286
287}
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