File: nii_3dto4d.pas

package info (click to toggle)
mricron 0.20140804.1~dfsg.1-3
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 13,508 kB
  • sloc: pascal: 114,876; sh: 49; makefile: 35
file content (456 lines) | stat: -rwxr-xr-x 14,773 bytes parent folder | download | duplicates (6)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
unit nii_3dto4d;
{$H+}


interface

uses
{$IFDEF FPC}gzio2,{$ENDIF}
  SysUtils,define_types,dicomtypes,niftiutil,prefs,classes,dialogs_msg, nifti_types;

function Stack3Dto4D(var lStr: TStringList; lOverwrite: boolean; lPrefs: TPrefs): boolean;
function ExtractNIFTIHdrs(var lStr: TStringList): boolean;

implementation
uses dialogsx;

function LeadingZeroFilename (lInX: string): string;
var
   lIn: string;
   lC,lnPad,lPos,lnDec,lExtPos,lLen: integer;
begin
     {$IFDEF Unix}
     lIn := lInX;
     {$ELSE}
     lIn := Lowercase(lInX);
     {$ENDIF}
     lnPad := 8;
     lLen := length(lIn);
     result := lIn;
     if lLen < 1 then exit;
     lExtPos := 1;
     while (lExtPos <= lLen) and (lIn[lExtPos] <> '.') do
           inc(lExtPos);
     if lExtPos <= 1 then
        exit;
     //lnDec := 0;
     lPos := lExtPos -1;
     while (lPos > 0) and ( lIn[lPos] in ['0'..'9']) do
           dec(lPos);
     lnDec := (lExtPos-lPos)-1;
     if (lnDec = 0) or (lnDec >= lnPad) then
        exit;
     result := '';
     if lPos > 0 then
        for lC := 1 to lPos do
            result := result + lIn[lC];
     for lC := 1 to (lnPad-lnDec) do
         result := result + '0';
     for lC := (lPos+1) to lLen do
         result := result+lIn[lC];
end;

procedure SortStrPadded (var lStr: TStringList);
//file1,file2...file10  not file1,file10..file2
//may be slow: not a great sorting algorithm
//may be inefficient: not sure if strings are exchanged or only pointers...
var counter, look:integer; temp:Tstrings;
begin
   if lStr.Count < 2 then exit;
   temp := TStringList.Create;
   for counter:=0 to lStr.Count-1 do
          temp.Append(LeadingZeroFilename{LowerCase}(lStr[counter]));
          for counter:=0 to temp.Count-1 do
               for look:=counter+1 to temp.Count-1 do
               if temp[look]<temp[counter] then begin
               lStr.Exchange(look, counter);
               temp.Exchange(look,counter);
     end;
     temp.Free;
end;

function PasStr (lStr: string): string; //removes nulls
var
   i: integer;
   t: string;
begin
     result := '';
     for i := 1 to length(lStr) do begin
         if (lStr[i] <> kDel) and(lStr[i] <> kTab) and (lStr[i] <> kEsc) and (lStr[i] <> chr(10)) and (lStr[i] <> chr (13)) and (ord(lStr[i]) <> 0) then
            result := result + lStr[i];
     end;
     result := '"'+result +'"'
end;

function NIIstr (lFileName: string; lHdr : TNIFTIhdr): string;
begin
     result := lFileName
     +kTab+'XYZT'+kTab+inttostr(lHdr.Dim[1])+kTab+inttostr(lHdr.Dim[2])+kTab+inttostr(lHdr.Dim[3])+kTab+inttostr(lHdr.Dim[4])
     +kTab+'XYZTmm'+kTab+floattostr(lHdr.PixDim[1])+kTab+floattostr(lHdr.PixDim[2])+kTab+floattostr(lHdr.PixDim[3])+kTab+floattostr(lHdr.PixDim[4])
     +kTab+'Description'+kTab+PasStr(lHdr.descrip)
     +kTab+'Data_Type'+kTab+PasStr(lHdr.Data_Type)
     +kTab+'db_name'+kTab+PasStr(lHdr.db_name)
     +kTab+'aux_file'+kTab+PasStr(lHdr.aux_file)
     +kTab+'intent_name'+kTab+PasStr(lHdr.intent_name)

     ;
end;

function ExtractNIFTIHdrs(var lStr: TStringList): boolean;
var
   lHdrName: string;
   lHdr : TNIFTIhdr;
   lByteSwap: boolean;
   lVol,lnVol : integer;
   lO: TNIIOpts;
begin
   result := false;
   lnVol := lStr.Count;
   if lnVol < 1 then
      exit;
   SortStrPadded(lStr);
   for lVol := 1 to lnVol do begin
       lHdrName := lStr[lVol-1];
       if not NIFTIhdr_LoadHdr (lHdrName, lHdr,lO) then
          dcmMsg('Unable to find '+lHdrName)
       else
           dcmMsg(NIIstr(lHdrName,lHdr));

       //dcmMsg( inttostr(lVol)+': '+lHdrName);
   end;
end;


function Stack3Dto4D(var lStr: TStringList; lOverwrite: boolean; lPrefs: TPrefs): boolean;
//function Reorder4D(var lHdrName: string; var lHdr: TNIFTIhdr; lOverwrite: boolean; lPrefs: TPrefs): boolean;
label 123;
var
   lOutBuffer,lIBuffer: byteP;
   lInOffset,lnVol,l4DVolBytes,l3DVolBytes,lIn3DBytes,l4DBytes,lVol,lInPos,lOutPos,lSlice: integer;
   lHdrName,lOutImgName: string;
   lHdr1,lHdr2,lOutHdr : TNIFTIhdr;
   lO: TNIIOpts;
   lPrefs4D: TPrefs;
begin
   result := false;
   lnVol := lStr.Count;
   if lnVol < 2 then begin
      dcmMsg('Stack 3D to 4D requires >1 volume');
      exit;
   end;
   SortStrPadded(lStr);
   lHdrName := lStr[0];
   NIFTIhdr_LoadHdr (lHdrName, lHdr1,lO);
   for lVol := 1 to lnVol do begin
       lHdrName := lStr[lVol-1];
       if not NIFTIhdr_LoadHdr (lHdrName, lHdr2,lO) then begin
          dcmMsg('Stack 3D to 4D unable to find '+lHdrName);
          exit;
       end;
       if (lHdr1.dim[4] > 1) then begin
          dcmMsg('Stack 3D to 4D aborted, image is already 4D: '+lHdrName );
          exit;
       end;
       if (lHdr1.dim[1] <> lHdr2.dim[1]) or (lHdr1.dim[2] <> lHdr2.dim[2]) or
          (lHdr1.dim[3] <> lHdr2.dim[3]) or (lHdr1.datatype <> lHdr2.datatype) then begin
          dcmMsg('Stack 3D to 4D aborted, image dimensions/datatype vary '+lHdrName + ' <> '+lStr[0]);
          exit;
       end;
       //dcmMsg( inttostr(lVol)+': '+lHdrName);
   end;
   lOutHdr := lHdr1;
   lOutHdr.dim[4] := lnVol;
   l3DVolBytes := lHdr1.dim[1]*lHdr1.dim[2]*lHdr1.dim[3]*(lHdr1.bitpix div 8);
   l4DVolBytes := l3DVolBytes * lnVol;
   GetMem(lOutBuffer,l4DVolBytes+kNIIImgOffset);

   dcmMsg('Order in output file:');
   lOutImgName := ChangeFilePrefix (lStr[0],'4D');
   lOutPos := kNIIImgOffset + 1;
   for lVol := 1 to lnVol do begin
       lHdrName := lStr[lVol-1];
       dcmMsg( inttostr(lVol)+': '+lHdrName);
       if not NIFTIhdr_LoadImg (lHdrName, lHdr2, lIBuffer, lInOffset,lO) then begin
          dcmMsg('3D -> 4D error loading image '+lHdrName);
          goto 123;
       end;
       Move(lIBuffer^[lInOffset+1],lOutBuffer^[lOutPos],l3DVolBytes);
       freemem(lIBuffer);
       lOutPos := lOutPos + l3DVolBytes;
   end;
   lPrefs4D := lPrefs;
   lPrefs4D.fourD := true;
   dcmMsg('4D image '+lOutImgName);
   if  SaveNIfTICore (lOutImgName, lOutBuffer, kNIIImgOffset+1, lOutHdr, lPrefs4D) = '' then begin
      dcmMsg('3D -> 4D Error');
      goto 123;
   end;

    freemem(lOutBuffer);
  result := true;
  exit;
123:
    freemem(lOutBuffer);
end;



(*function Reorder4D(var lHdrName: string; var lHdr: TNIFTIhdr; lByteSwap,lSPM2in,lSingleNIIFile,lGZ,lOverwrite: boolean): boolean;
var
   lOutHdr: TNIFTIhdr;
   lInName,lImgName: string;
   lPos,lSlice,lVol,lInVolBytes,lSliceBytes: integer;
   lBuffer: bytep;
   lGZi,lSPM2: boolean;
   lOutF,lInF: File;
begin
   result := false;
   lGZi := lGZ;
   lSPM2 := lSPM2in;
   if lSingleNIIFIle then
      lSPM2 := false;
   if (lHdr.dim[4] < 2) or (lHdr.dim[3] < 2) then
      exit;
   lOutHdr := lHdr;
   lOutHdr.dim[4] := lHdr.dim[3];
   lOutHdr.dim[3] := lHdr.dim[4];
   lSliceBytes := lHdr.dim[1]*lHdr.dim[2]*(lHdr.bitpix div 8);
   lInVolBytes := lSliceBytes*lHdr.dim[3];
   GetMem(lBuffer,lSliceBytes);
   if UpCaseExt(lHdrName) ='.HDR' then begin
       if lOverwrite then
          deletefile(lHdrName);
       lInName :=  changefileext(lHdrName,'.img')
   end else begin
       lOutHdr.vox_offset := 352;
       lInName := lHdrName;
   end;
   if not fileexists(lInName) then begin
       dcmMsg('4Dclip Error: Unable to find '+lInName);
       exit;
   end;
   if FSize (lInName) < ( (lInVolBytes*lHdr.dim[4])+round(lHdr.vox_offset)) then begin
       dcmMsg('4Dclip Error: File smaller than expected (can not convert compressed) '+lInName);
       exit;
   end;
   dcmMsg('Reordering image');
   if not lSingleNiiFile then begin
       lHdrName :=  changefileext(lHdrName,'.hdr');
       lImgName :=  changefileext(lHdrName,'.img');
       lGZi := false;
   end else begin
       lHdrName :=  changefileext(lHdrName,'.nii');
       lImgName :=  changefileext(lHdrName,'.nii');
   end;
   if lOverwrite then begin
      renamefile(lInName,changefileext(lInName,'.tmp'));
      lInName := changefileext(lInName,'.tmp');
   end else begin
       lHdrName := ChangeFilePrefixExt (lHdrName,'x');
       lImgName := ChangeFilePrefixExt (lImgName,'x');
       dcmMsg('saving as '+lHdrName);
   end;
   AssignFile(lInF, lInName);
   Reset(lInF,1);
   Seek(lInF,round(lHdr.vox_offset));
   SaveHdr (lHdrName,lOutHdr,lByteSwap{ false},lSPM2);
   AssignFile(lOutF, lImgName);
   if lSingleNIIFile then begin
      Reset(lOutF,1);
      Seek(lOutF,352);
   end else
       Rewrite(lOutF,1);
   for lVol := 1 to  lOutHdr.dim[4] do begin
       lPos := ((lVol-1)*lSliceBytes) + round(lHdr.vox_offset);
       for lSlice := 1 to lOutHdr.dim[3] do begin
           Filemode := 0;  //ReadONly
           seek(lInF,lPos);
           BlockRead(lInF, lBuffer^, lSliceBytes);
           Filemode := 2;
           BlockWrite(lOutF, lBuffer^, lSliceBytes);
           lPos := lPos + lInVolBytes;
       end;//for lslice
   end; //for lvol
   CloseFile(lInF);
   CloseFile(lOutF);
   Freemem(lBuffer);
   if lOverwrite then
      DeleteFile(lInName);
   if lGZi then
      GZipFile(lImgName,lImgName+'.gz',true);
   result := true;
end;      *)

(*function Clip4D(var lHdrName: string; var lHdr: TNIFTIhdr;  lByteSwap,lSPM2in, lSingleNIIFile,lGZ,lOverwrite: boolean; lStartIn,lEndIn: integer ): string;
var
   lOutHdr: TNIFTIhdr;
   lInName,lImgName: string;
   lVol,lVolBytes,lStart,lEnd: integer;
    lBuffer: bytep;
    lGZi,lSPM2 : boolean;
    lOutF,lInF: File;
begin
   result := '';
   lGZi := lGZ;
   lSPM2 := lSPM2in;
   if lSingleNIIFIle then
      lSPM2 := false;
   lStart := lStartIn;
   if lStart < 0 then
      lStart := 0;
   lEnd := lEndIn;
   if lEnd < 0 then
      lEnd := 0;
   lOutHdr := lHdr;
   lOutHdr.dim[4] := lOutHdr.dim[4]-lStart-lEnd;
   if lOutHdr.dim[4] < 1 then
      exit;
   lVolBytes := lOutHdr.dim[1]*lOutHdr.dim[2]*lOutHdr.dim[3]*(lOutHdr.bitpix div 8);
   GetMem(lBuffer,lVolBytes);
   if UpCaseExt(lHdrName) ='.HDR' then begin
       if lOverwrite then
          deletefile(lHdrName);
       lInName :=  changefileext(lHdrName,'.img')
   end else begin
       lOutHdr.vox_offset := 352;
       lInName := lHdrName;
   end;
   if not fileexists(lInName) then begin
       dcmMsg('4Dclip Error: Unable to find '+lInName);
       exit;
   end;
   if FSize (lInName) < ( (lVolBytes*lHdr.dim[4])+round(lHdr.vox_offset)) then begin
       dcmMsg('4Dclip Error: File smaller than expected (can not convert compressed) '+lInName);
       exit;
   end;
   if (lStart > 0) or (lEnd > 0) then
      dcmMsg('4D clip - removing first '+inttostr(lStart)+' and last '+inttostr(lEnd) +' volumes')
   else
       dcmMsg('Formatting image');
   if not lSingleNiiFile then begin
       lGZi := false;
       lHdrName :=  changefileext(lHdrName,'.hdr');
       lImgName :=  changefileext(lHdrName,'.img');
   end else begin
       lHdrName :=  changefileext(lHdrName,'.nii');
       lImgName :=  changefileext(lHdrName,'.nii');
   end;
   if lOverwrite then begin
      renamefile(lInName,changefileext(lInName,'.tmp'));
      lInName := changefileext(lInName,'.tmp');
   end else begin
       lHdrName := ChangeFilePrefixExt (lHdrName,'x');
       lImgName := ChangeFilePrefixExt (lImgName,'x');
       dcmMsg('Saving clipped as '+lHdrName);
   end;
   AssignFile(lInF, lInName);
   Reset(lInF,1);
   Seek(lInF,round(lHdr.vox_offset));
   SaveHdr (lHdrName,lOutHdr, lByteSwap{false},lSPM2);
   AssignFile(lOutF, lImgName);
   if lSingleNIIFile then begin
      Reset(lOutF,1);
      Seek(lOutF,352);
   end else
       Rewrite(lOutF,1);
   for lVol := 1 to (lHdr.dim[4]-lEnd) do begin
       //1st - save header
       Filemode := 0;  //ReadONly
       BlockRead(lInF, lBuffer^, lVolBytes);
       if (lVol > lStart) then begin
          Filemode := 2;
          BlockWrite(lOutF, lBuffer^, lVolBytes);
       end;
   end;
   CloseFile(lInF);
   CloseFile(lOutF);
   Freemem(lBuffer);
   if lOverwrite then
      DeleteFile(lInName);
   if lGZi then begin
      lHdrName := lImgName+'.gz';
      GZipFile(lImgName,lHdrName,true);
   end;
   result := lHdrName;
end;

function Convert4Dto3D(var lHdrName: string; var lHdr: TNIFTIhdr; lByteSwap, lSPM2in,lSingleNIIFile,lGZ: boolean ): boolean;
var
   lOutHdr: TNIFTIhdr;
   lOutName,lImgName: string;
   lVol,lVolBytes: integer;
    lBuffer: bytep;
    lSPM2,lGZi: boolean;
     lOutF,lInF: File;
begin
   result := false;
   lSPM2 := lSPM2in;
   if lSingleNIIFIle then
      lSPM2 := false;
   lGZi := lGZ;
   if lHdr.dim[4] < 2 then
      exit;
   lOutHdr := lHdr;
   lOutHdr.dim[0] := 3;//3D
   lOutHdr.dim[4] := 1;
   lVolBytes := lOutHdr.dim[1]*lOutHdr.dim[2]*lOutHdr.dim[3]*(lOutHdr.bitpix div 8);
   GetMem(lBuffer,lVolBytes);
   //lSingleNIIFile := true;
   if UpCaseExt(lHdrName) ='.HDR' then begin
       //lSingleNIIFile := false;
       lImgName :=  changefileext(lHdrName,'.img')
   end else
       lImgName := lHdrName;
   if not fileexists(lImgName) then begin
       dcmMsg('4D->3D Error: Unable to find '+lImgName);
       exit;
   end;
   if FSize (lImgName) < ( (lVolBytes*lHdr.dim[4])+round(lHdr.vox_offset)) then begin
       dcmMsg('4D->3D Error: File smaller than expected (can not convert compressed) '+lImgName);
       exit;
   end;
   //dcmMsg(inttostr(round(lHdr.vox_offset)));
   AssignFile(lInF, lImgName);
   Reset(lInF,1);
   Seek(lInF,round(lHdr.vox_offset));
   if not lSingleNiiFile then begin
       lGZi := false;
       lHdrName :=  changefileext(lHdrName,'.hdr');
       lImgName :=  changefileext(lHdrName,'.img');
   end else begin
       lHdrName :=  changefileext(lHdrName,'.nii');
       lImgName :=  changefileext(lHdrName,'.nii');
   end;
   for lVol := 1 to lHdr.dim[4] do begin
       //1st - save header
       lOutName := AddFileNum(lVol,lHdr.dim[4],lHdrName);
       SaveHdr (lOutName,lOutHdr,lByteSwap {false},lSPM2);
       Filemode := 0;  //ReadONly
       BlockRead(lInF, lBuffer^, lVolBytes);

       lOutName := AddFileNum(lVol,lHdr.dim[4],lImgName);
       Filemode := 2;
       AssignFile(lOutF, lOutName);
       if (lSingleNIIFile) and (not lSPM2) then begin
		Reset(lOutF,1);
		Seek(lOutF,352);
       end else
		Rewrite(lOutF,1);
       BlockWrite(lOutF, lBuffer^, lVolBytes);
       CloseFile(lOutF);
       if lGZi then begin
          GZipFile(lOutName,lOutName+'.gz',true);
          //DeleteFile(lOutName);
       end;
   end;
   CloseFile(lInF);
   Freemem(lBuffer);
   //if lDeleteOrig then begin
      DeleteFile(lHdrName);
      if not lSingleNIIFile then
         DeleteFile(lImgName);
   //end;
end;       *)


end.