Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/11/07 09:50:52 $
- Version: $Revision: 1.79 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.93 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmDictSet.h"
#include "gdcmOrientation.h"
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
+
#include <fstream>
/*
namespace gdcm
{
+typedef std::map<uint16_t, int> GroupHT; // Hash Table
//-------------------------------------------------------------------------
// Constructor / Destructor
/**
Initialize();
if ( FileInternal->IsReadable() )
{
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
}
}
if ( !FileInternal->Load() )
return false;
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
return true;
}
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
+ * \brief Accesses an existing DataEntry through it's (group, element)
+ * and modifies it's content with the given value.
* @param content new value (string) to substitute with
* @param group group number of the Dicom Element to modify
* @param elem element number of the Dicom Element to modify
- * \return false if DocEntry not found
+ * \return false if DataEntry not found
*/
bool FileHelper::SetEntryString(std::string const &content,
uint16_t group, uint16_t elem)
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
+ * \brief Accesses an existing DataEntry through it's (group, element)
+ * and modifies it's content with the given value.
* @param content new value (void* -> uint8_t*) to substitute with
* @param lgth new value length
* @param group group number of the Dicom Element to modify
* @param elem element number of the Dicom Element to modify
- * \return false if DocEntry not found
+ * \return false if DataEntry not found
*/
bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth,
uint16_t group, uint16_t elem)
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it with the given value when unexistant.
- * @param content (string)value to be set
+ * \brief Modifies the value of a given DataEntry when it exists.
+ * Creates it with the given value when unexistant.
+ * @param content (string) value to be set
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryString(std::string const &content,
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it with the given value when unexistant.
+ * \brief Modifies the value of a given DataEntry when it exists.
+ * Creates it with the given value when unexistant.
* A copy of the binArea is made to be kept in the Document.
* @param binArea (binary)value to be set
* @param lgth new value length
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it, empty (?!) when unexistant.
+ * \brief Adds an empty SeqEntry
+ * (remove any existing entry with same group,elem)
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * \return pointer to the created SeqEntry (NULL when creation
* failed).
*/
SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem)
* - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
* @return Pointer to newly allocated pixel data.
* (uint8_t is just for prototyping. feel free to cast)
- * NULL if alloc fails
+ * NULL if alloc fails
*/
uint8_t *FileHelper::GetImageDataRaw ()
{
#ifndef GDCM_LEGACY_REMOVE
/*
- * \ brief Useless function, since PixelReadConverter forces us
+ * \brief Useless function, since PixelReadConverter forces us
* copy the Pixels anyway.
* Reads the pixels from disk (uncompress if necessary),
* Transforms YBR pixels, if any, into RGB pixels
* Transforms single Grey plane + 3 Palettes into a RGB Plane
* Copies at most MaxSize bytes of pixel data to caller allocated
* memory space.
- * \ warning This function allows people that want to build a volume
+ * \warning This function allows people that want to build a volume
* from an image stack *not to* have, first to get the image pixels,
* and then move them to the volume area.
* It's absolutely useless for any VTK user since vtk chooses
* to load the image line by line, starting from the end.
* VTK users have to call GetImageData
*
- * @ param destination Address (in caller's memory space) at which the
+ * @param destination Address (in caller's memory space) at which the
* pixel data should be copied
- * @ param maxSize Maximum number of bytes to be copied. When MaxSize
+ * @param maxSize Maximum number of bytes to be copied. When MaxSize
* is not sufficient to hold the pixel data the copy is not
* executed (i.e. no partial copy).
- * @ return On success, the number of bytes actually copied. Zero on
+ * @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize)
break;
case JPEG:
SetWriteFileTypeToJPEG();
- std::cerr << "Writting as JPEG" << std::endl;
break;
}
CheckMandatoryElements();
}
/**
- * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ * \brief Sets in the File the TransferSyntax to 'JPEG'
*/
void FileHelper::SetWriteFileTypeToJPEG()
{
tss->Delete();
}
+/**
+ * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ */
void FileHelper::SetWriteFileTypeToExplicitVR()
{
std::string ts = Util::DicomString(
/**
* \brief This method is called automatically, just before writting
- * in order to produce a 'True Dicom V3' image
+ * in order to produce a 'True Dicom V3' image.
+ *
* We cannot know *how* the user made the File :
* (reading an old ACR-NEMA file or a not very clean DICOM file ...)
- *
* Just before writting :
* - we check the Entries
* - we create the mandatory entries if they are missing
* The writing process will restore the entries as they where before
* entering FileHelper::CheckMandatoryElements, so the user will always
* see the entries just as they were before he decided to write.
+ *
* \note
* - Entries whose type is 1 are mandatory, with a mandatory value
* - Entries whose type is 1c are mandatory-inside-a-Sequence,
* with an optional value
* - Entries whose type is 3 are optional
*
- * \todo : - warn the user if we had to add some entries :
+ * \todo
+ * - warn the user if we had to add some entries :
* even if a mandatory entry is missing, we add it, with a default value
* (we don't want to give up the writting process if user forgot to
* specify Lena's Patient ID, for instance ...)
/* -------------------------------------------------------------------------------------
To be moved to User's guide / WIKI ?
+We have to deal with 4 *very* different cases :
+-1) user created ex nihilo his own image and wants to write it as a Dicom image.
+-2) user modified the pixels of an existing image.
+-3) user created a new image, using existing images (eg MIP, MPR, cartography image)
+-4) user anonymized an image without processing the pixels.
+
+gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases.
+
+1)2)3)4)
+0008 0012 Instance Creation Date
+0008 0013 Instance Creation Time
+0008 0018 SOP Instance UID
+are *always* created with the current values; user has *no* possible intervention on
+them.
+
+'Serie Instance UID'(0x0020,0x000e)
+'Study Instance UID'(0x0020,0x000d) are kept as is if already exist,
+ created if it doesn't.
+ The user is allowed to create his own Series/Studies,
+ keeping the same 'Serie Instance UID' / 'Study Instance UID' for various images
+ Warning :
+ The user shouldn't add any image to a 'Manufacturer Serie'
+ but there is no way no to allowed him to do that
+
+ None of the 'shadow elements' are droped out.
+
+
+1)
+'Modality' (0x0008,0x0060) is defaulted to "OT" (other) if missing.
+'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image).
+'Study Date', 'Study Time' are defaulted to current Date and Time.
+
+1)2)3)
+'Media Storage SOP Class UID' (0x0002,0x0002)
+'SOP Class UID' (0x0008,0x0016) are set to
+ [Secondary Capture Image Storage]
+'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY"
+Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image)
+
+2)4)
+If 'SOP Class UID' exists in the native image ('true DICOM' image)
+ we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
+ --> 'Referenced SOP Class UID' (0x0008, 0x1150)
+ whose value is the original 'SOP Class UID'
+ --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
+ whose value is the original 'SOP Class UID'
+
+3) TODO : find a trick to allow user to pass to the writter the list of the Dicom images
+ or the Series, (or the Study ?) he used to created his image
+ (MIP, MPR, cartography image, ...)
+ These info should be stored (?)
+ 0008 1110 SQ 1 Referenced Study Sequence
+ 0008 1115 SQ 1 Referenced Series Sequence
+ 0008 1140 SQ 1 Referenced Image Sequence
+
+4) When user *knows* he didn't modified the pixels, he may ask the writer to keep some
+informations unchanged :
+'Media Storage SOP Class UID' (0x0002,0x0002)
+'SOP Class UID' (0x0008,0x0016)
+'Image Type' (0x0008,0x0008)
+'Conversion Type' (0x0008,0x0064)
+He has to use gdcm::FileHelper::SetKeepMediaStorageSOPClassUID(true)
+(probabely name has to be changed)
+
+
+Bellow follows the full description (hope so !) of the consistency checks performed
+by gdcm::FileHelper::CheckMandatoryElements()
-->'Media Storage SOP Class UID' (0x0002,0x0002)
(The written image is no longer an 'ORIGINAL' one)
Except if user told he wants to keep MediaStorageSOPClassUID,
when *he* knows he didn't modify the image (e.g. : he just anonymized the file)
-
+
+ --> Conversion Type (0x0008,0x0064)
+ is forced to 'SYN' (Synthetic Image)
+ Except if user told he wants to keep MediaStorageSOPClassUID,
+ when *he* knows he didn't modify the image (e.g. : he just anonymized the file)
+
--> 'Modality' (0x0008,0x0060)
is defaulted to "OT" (other) if missing.
(a fully user created image belongs to *no* modality)
--> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency
--> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0"
--> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale)
+
--> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value
---> Instance Creation Date, Instance Creation Time, Study Date, Study Time
- are force to current Date and Time
-
---> Conversion Type (0x0008,0x0064)
- is forced to 'SYN' (Synthetic Image)
+--> Instance Creation Date, Instance Creation Time are forced to current Date and Time
+
+--> Study Date, Study Time are defaulted to current Date and Time
+ (they remain unchanged if they exist)
--> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
- Image Orientation (Patient) : (0020|0037)
+ Image Orientation (Patient) : (0020|0037) or from
+ Image Orientation (RET) : (0020 0035)
--> Study ID, Series Number, Instance Number, Patient Orientation (Type 2)
are created, with empty value if there are missing.
}
std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
- if ( pixelSpacing == GDCM_UNKNOWN )
+ if ( pixelSpacing == GDCM_UNFOUND )
+ {
pixelSpacing = "1.0\\1.0";
- else
// if missing, Pixel Spacing forced to "1.0\1.0"
- CopyMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
-
+ CopyMandatoryEntry(0x0028,0x0030,pixelSpacing);
+ }
+
// 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
// --> This one is the *legal* one !
// FIXME : we should write it only when we are *sure* the image comes from
- // an imager (see also 0008,0x0064)
-
+ // an imager (see also 0008,0x0064)
CheckMandatoryEntry(0x0018,0x1164,pixelSpacing);
-
+
// Samples Per Pixel (type 1) : default to grayscale
CheckMandatoryEntry(0x0028,0x0002,"1");
CopyMandatoryEntry(0x0008,0x0013,time);
// Study Date
- CopyMandatoryEntry(0x0008,0x0020,date);
+ CheckMandatoryEntry(0x0008,0x0020,date);
// Study Time
- CopyMandatoryEntry(0x0008,0x0030,time);
+ CheckMandatoryEntry(0x0008,0x0030,time);
// Accession Number
//CopyMandatoryEntry(0x0008,0x0050,"");
// Patient Orientation
// Can be computed from (0020|0037) : Image Orientation (Patient)
- gdcm::Orientation o;
- std::string ori = o.GetOrientation ( FileInternal );
- if (ori != "\\" )
+ gdcm::Orientation *o = gdcm::Orientation::New();
+ std::string ori = o->GetOrientation ( FileInternal );
+ o->Delete();
+ if (ori != "\\" && ori != GDCM_UNFOUND)
CheckMandatoryEntry(0x0020,0x0020,ori);
else
CheckMandatoryEntry(0x0020,0x0020,"");
// Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
CheckMandatoryEntry(0x0008,0x0090,"");
- // Remove some inconstencies (probably some more will be added)
-
- // if (0028 0008)Number of Frames exists
- // Push out (0020 0052),Frame of Reference UID
- // (only meaningfull within a Serie)
- DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008);
- if ( !e_0028_0008 )
- {
- Archive->Push(0x0020, 0x0052);
- }
-
// Deal with element 0x0000 (group length) of each group.
// First stage : get all the different Groups
+ /*
GroupHT grHT;
- DocEntry *d=input->GetFirstEntry();
+ DocEntry *d = FileInternal->GetFirstEntry();
while(d)
{
grHT[d->GetGroup()] = 0;
- d=input->GetNextEntry();
+ d=FileInternal->GetNextEntry();
}
// Second stage : add the missing ones (if any)
for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it)
CheckMandatoryEntry(it->first, 0x0000, "0");
}
// Third stage : update all 'zero level' groups length
-
+*/
}
void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
Archive->Restore(0x0020,0x000e);
}
+
+/**
+ * \brief CallStartMethod
+ */
+void FileHelper::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
+}
+
+/**
+ * \brief CallProgressMethod
+ */
+void FileHelper::CallProgressMethod()
+{
+ CommandManager::ExecuteCommand(this,CMD_PROGRESS);
+}
+
+/**
+ * \brief CallEndMethod
+ */
+void FileHelper::CallEndMethod()
+{
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
+}
+
//-----------------------------------------------------------------------------
// Private
/**
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff