From f9ca20b91e15d47cb0142c6ba1a7be5d1ffc252e Mon Sep 17 00:00:00 2001 From: pierre gueth Date: Mon, 24 Oct 2011 11:46:44 +0200 Subject: [PATCH] reading for gate ascii format --- common/clitkGateAsciiImageIO.cxx | 178 +++++++++++-------------------- 1 file changed, 64 insertions(+), 114 deletions(-) diff --git a/common/clitkGateAsciiImageIO.cxx b/common/clitkGateAsciiImageIO.cxx index 02250cb..af42c05 100644 --- a/common/clitkGateAsciiImageIO.cxx +++ b/common/clitkGateAsciiImageIO.cxx @@ -44,22 +44,44 @@ std::ostream& operator<<(std::ostream& os, const clitk::GateAsciiImageIO::GateAs // Read Image Information void clitk::GateAsciiImageIO::ReadImageInformation() { - itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName); + FILE* handle = fopen(m_FileName.c_str(),"r"); + if (!handle) { + itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName); + return; + } + + GateAsciiHeader header; + if (!ReadHeader(handle,header)) { + itkGenericExceptionMacro(<< "Could not read header: " << m_FileName); + fclose(handle); + return; + } + fclose(handle); + + int real_length = -1; + double real_spacing = 0; + for (int kk=0; kk<3; kk++) { + if (header.resolution[kk]>1) { + if (real_length>0) { + itkGenericExceptionMacro(<< "Could not image dimension: " << m_FileName); + return; + } + real_length = header.resolution[kk]; + real_spacing = header.voxel_size[kk]; + } + } + assert(real_length == header.nb_value); - /* Convert hnd to ITK image information */ + // Set image information SetNumberOfDimensions(2); - //SetDimensions(0, hnd.SizeX); - //SetDimensions(1, hnd.SizeY); - //SetSpacing(0, hnd.dIDUResolutionX); - //SetSpacing(1, hnd.dIDUResolutionY); - //SetOrigin(0, -0.5*(hnd.SizeX-1)*hnd.dIDUResolutionX); //SR: assumed centered - //SetOrigin(1, -0.5*(hnd.SizeY-1)*hnd.dIDUResolutionY); //SR: assumed centered - //SetComponentType(itk::ImageIOBase::UINT); - - /* Store important meta information in the meta data dictionary */ - //itk::EncapsulateMetaData(this->GetMetaDataDictionary(), "dCTProjectionAngle", hnd.dCTProjectionAngle); - //itk::ExposeMetaData( this->GetMetaDataDictionary(), &(hnd.dCTProjectionAngle), "dCTProjectionAngle"); + SetDimensions(0, real_length); + SetDimensions(1, 1); + SetSpacing(0, real_spacing); + SetSpacing(1, 1); + SetOrigin(0, 0); + SetOrigin(1, 0); + SetComponentType(itk::ImageIOBase::DOUBLE); } //-------------------------------------------------------------------- @@ -136,15 +158,15 @@ bool clitk::GateAsciiImageIO::ReadHeader(FILE* handle, GateAsciiHeader& header) { // build regex int ret = 0; ret = regcomp(&re_comment,"^#.+$",REG_EXTENDED|REG_NEWLINE); - assert(ret); + assert(ret == 0); ret = regcomp(&re_matrix_size,"^# +Matrix *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE); - assert(ret); + assert(ret == 0); ret = regcomp(&re_resol,"^# +Resol *= +\\(([0-9]+),([0-9]+),([0-9]+)\\)$",REG_EXTENDED|REG_NEWLINE); - assert(ret); + assert(ret == 0); ret = regcomp(&re_voxel_size,"^# +Voxel *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE); - assert(ret); + assert(ret == 0); ret = regcomp(&re_nb_value,"^# +nbVal *= +([0-9]+)$",REG_EXTENDED|REG_NEWLINE); - assert(ret); + assert(ret == 0); } if (!ReadLine(handle,line)) return false; @@ -180,107 +202,35 @@ bool clitk::GateAsciiImageIO::ReadHeader(FILE* handle, GateAsciiHeader& header) //-------------------------------------------------------------------- // Read Image Content -void clitk::GateAsciiImageIO::Read(void * buffer) +void clitk::GateAsciiImageIO::Read(void* abstract_buffer) { - FILE *fp; - - uint32_t* buf = (uint32_t*)buffer; - unsigned char *pt_lut; - uint32_t a; - float b; - unsigned char v; - int lut_idx, lut_off; - size_t num_read; - char dc; - short ds; - long dl, diff=0; - uint32_t i; - - fp = fopen (m_FileName.c_str(), "rb"); - if (fp == NULL) - itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName); - - pt_lut = (unsigned char*) malloc (sizeof (unsigned char) * GetDimensions(0) * GetDimensions(1)); - - /* Read LUT */ - fseek (fp, 1024, SEEK_SET); - fread (pt_lut, sizeof(unsigned char), (GetDimensions(1)-1)*GetDimensions(0) / 4, fp); - - /* Read first row */ - for (i = 0; i < GetDimensions(0); i++) { - fread (&a, sizeof(uint32_t), 1, fp); - buf[i] = a; - b = a; - } - - /* Read first pixel of second row */ - fread (&a, sizeof(uint32_t), 1, fp); - buf[i++] = a; - b = a; - - /* Decompress the rest */ - lut_idx = 0; - lut_off = 0; - while (i < GetDimensions(0) * GetDimensions(1)) { - uint32_t r11, r12, r21; - - r11 = buf[i-GetDimensions(0)-1]; - r12 = buf[i-GetDimensions(0)]; - r21 = buf[i-1]; - v = pt_lut[lut_idx]; - switch (lut_off) { - case 0: - v = v & 0x03; - lut_off ++; - break; - case 1: - v = (v & 0x0C) >> 2; - lut_off ++; - break; - case 2: - v = (v & 0x30) >> 4; - lut_off ++; - break; - case 3: - v = (v & 0xC0) >> 6; - lut_off = 0; - lut_idx ++; - break; - } - switch (v) { - case 0: - num_read = fread (&dc, sizeof(unsigned char), 1, fp); - if (num_read != 1) goto read_error; - diff = dc; - break; - case 1: - num_read = fread (&ds, sizeof(unsigned short), 1, fp); - if (num_read != 1) goto read_error; - diff = ds; - break; - case 2: - num_read = fread (&dl, sizeof(uint32_t), 1, fp); - if (num_read != 1) goto read_error; - diff = dl; - break; + FILE* handle = fopen(m_FileName.c_str(),"r"); + if (!handle) { + itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName); + return; } - buf[i] = r21 + r12 + diff - r11; - b = buf[i]; - i++; - } - - /* Clean up */ - free (pt_lut); - fclose (fp); - return; + GateAsciiHeader header; + if (!ReadHeader(handle,header)) { + itkGenericExceptionMacro(<< "Could not read header: " << m_FileName); + fclose(handle); + return; + } -read_error: + { + double* buffer = static_cast(abstract_buffer); + int read_count = 0; + while (true) { + std::string line; + if (!ReadLine(handle,line)) break; + *buffer = ConvertFromString(line); + read_count++; + buffer++; + } + assert(read_count == header.nb_value); + } - itkGenericExceptionMacro(<< "Error reading gate ascii file"); - free (pt_lut); - fclose (fp); - return; + fclose(handle); } //-------------------------------------------------------------------- -- 2.45.1