void TestFileGenerator::WriteSmallCelFileNoStdev() { CelFileData data("small_cel_file_no_stdev"); data.SetIntensityCount(25); data.SetStdDevCount(0); data.SetPixelCount(25); data.SetOutlierCount(2); data.SetMaskCount(3); data.SetRows(5); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; Int16Vector vPixels; for (int i=0; i<25; ++i) { vInten.push_back(100.0f*i); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WritePixels(vPixels); // XYCoordVector XYCoordVector outlier; XYCoord xy(0,0); outlier.push_back(xy); xy.xCoord = 1; xy.yCoord = 2; outlier.push_back(xy); writer->WriteOutlierCoords(outlier); XYCoordVector masked; xy.xCoord = 1; xy.yCoord = 0; masked.push_back(xy); xy.xCoord = 2; xy.yCoord = 1; masked.push_back(xy); xy.xCoord = 3; xy.yCoord = 2; masked.push_back(xy); writer->WriteMaskCoords(masked); delete writer; }
void CHPData::SetFloatToGenericHdr(const std::wstring& name, float value) { ParameterNameValueType paramType; paramType.SetName(name); paramType.SetValueFloat(value); GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); hdr->AddNameValParam(paramType); }
void TestFileGenerator::WriteCelFileWithADataSetWithZeroRows() { CelFileData data("small_cel_file_with_dataset_of_zero_rows"); data.SetIntensityCount(25); data.SetStdDevCount(25); data.SetPixelCount(25); data.SetOutlierCount(0); data.SetMaskCount(0); data.SetRows(5); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; FloatVector vStdev; Int16Vector vPixels; for (int i=0; i<25; ++i) { vInten.push_back(100.0f*i); vStdev.push_back(.123f); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WriteStdDevs(vStdev); writer->WritePixels(vPixels); XYCoordVector outlier; writer->WriteOutlierCoords(outlier); XYCoordVector masked; writer->WriteMaskCoords(masked); delete writer; }
void TestFileGenerator::WriteOutGenericDATDataFileNoGrid() { GenericDataHeader gdh; AddStandardGenericDataHeader(gdh); // Fill the DataGroupHeader DataGroupHeader dch; dch.SetName(L"First Data Cube"); // Fill the DataSetHeader DataSetHeader dph; dph.SetName(L"acquired data"); ParameterNameValueType nvt; nvt.SetName(L"Scanner"); nvt.SetValueText(L"M10"); dph.AddNameValParam(nvt); nvt.SetName(L"Pixel Size"); nvt.SetValueFloat(0.051f); dph.AddNameValParam(nvt); dph.AddColumn(UShortColumn(L"Pixel")); int32_t rows = 100; dph.SetRowCnt(rows); dch.AddDataSetHdr(dph); // Set the FileHeader FileHeader fh; fh.SetFilename("test.file.data_dat"); fh.SetGenericDataHdr(gdh); fh.AddDataGroupHdr(dch); // Create the generic file writer GenericFileWriter gfWriter(&fh); gfWriter.WriteHeader(); DataGroupWriterIt dcwBegin, dcwEnd; gfWriter.GetDataGroupWriters(dcwBegin, dcwEnd); DataGroupWriter d = *dcwBegin; dcwBegin->WriteHeader(); DataSetWriterIt dpwBegin, dpwEnd; dcwBegin->GetDataSetWriters(dpwBegin, dpwEnd); dpwBegin->WriteHeader(); // Write out the data for( int32_t i=0; i < rows; ++i ) { u_int16_t value = (u_int16_t)(i*10+i); dpwBegin->Write(value); } dpwBegin->UpdateNextDataSetOffset(); dcwBegin->Close(); }
void DATFileUpdaterTest::AddParameters(DATData& data) { ParameterNameValueType nvt; nvt.SetName(L"Santa Clara"); nvt.SetValueUInt8(56); data.AddGridAlignmentAlgorithmParameter(nvt); nvt.SetName(L"San Mateo"); nvt.SetValueFloat(4.56f); data.AddGridAlignmentAlgorithmParameter(nvt); }
void TestFileGenerator::WriteSmallCelFileNoOutlierNoMask() { CelFileData data("small_cel_file_no_outlier_no_mask"); data.SetIntensityCount(10); data.SetStdDevCount(10); data.SetPixelCount(10); data.SetOutlierCount(0); data.SetMaskCount(0); data.SetRows(2); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; FloatVector vStdev; Int16Vector vPixels; for (int i=0; i<10; ++i) { vInten.push_back(100.0f*i); vStdev.push_back(.5*i); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WriteStdDevs(vStdev); writer->WritePixels(vPixels); delete writer; }
/** * No more probesets will be processed, this is a chance to finish outputting * results and clean up. * @param qMethod - Quantification method that was used. * @return true if success, false otherwise. */ bool QuantMethodExprCCCHPReport::finish(QuantMethod &qMethod) { // Sanity to check we saw all the probe sets we were expecting. if (m_CurrentProbeSetCount != m_Info.m_NumProbeSets) { Err::errAbort("QuantMethodExprCCCHPReport::finish() - Expecting: " + ToStr(m_Info.m_NumProbeSets) + " but got: " + ToStr(m_CurrentProbeSetCount) + ". Command Console CHP file will be corrupt."); } // Flush remaining signal entries in the buffer. m_ExpressionQuantificationBufferWriter.FlushBuffer(); // Rewrite CHP files to get chip summary entires Verbose::out(1,"Creating final files for CHP output"); Verbose::progressBegin(1, ToStr("Finalizing Expression CHP Files"), m_CHPFileNames.size(), 1, m_CHPFileNames.size()); try { for (unsigned int chip = 0; chip < m_CHPFileNames.size(); chip++) { // open up tmp chp file to pull results from GenericData data; GenericFileReader reader; std::string filename = m_CHPFileNames[chip]+".tmp"; reader.SetFilename(filename); reader.ReadHeader(data); GenericDataHeader* hdr = data.Header().GetGenericDataHdr(); GenericDataHeader updateHdr; for (int source = 0; source < m_ChipSummaries.size(); source++) { ChipSummary::metricDefVec_t metricDefs = m_ChipSummaries[source]->getMetricDefs(); for (int i = 0; i < metricDefs.size(); i++) { ChipSummary::Metric metric; if (!m_ChipSummaries[source]->getMetric(chip, metricDefs[i].m_name, metric)) { Err::errAbort("QuantMethodExprCCCHPReport: metric '" + metricDefs[i].m_name + "' was not found"); } std::wstring mName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX); mName += StringUtils::ConvertMBSToWCS(metric.m_Name); ParameterNameValueType param; if (hdr->FindNameValParam(mName, param) == false) { Err::errAbort("QuantMethodExprCCCHPReport: metric name '" + StringUtils::ConvertWCSToMBS(mName) + "' could not be found in the header of " + filename); } switch (param.GetParameterType()) { case ParameterNameValueType::Int8Type: param.SetValueInt8((int8_t)metric.m_Integer); break; case ParameterNameValueType::UInt8Type: param.SetValueUInt8((u_int8_t)metric.m_Integer); break; case ParameterNameValueType::Int16Type: param.SetValueInt16((int16_t)metric.m_Integer); break; case ParameterNameValueType::UInt16Type: param.SetValueUInt16((u_int16_t)metric.m_Integer); break; case ParameterNameValueType::Int32Type: param.SetValueInt32((int32_t)metric.m_Integer); break; case ParameterNameValueType::UInt32Type: param.SetValueUInt32((u_int32_t)metric.m_Integer); break; case ParameterNameValueType::FloatType: param.SetValueFloat((float)metric.m_Double); break; case ParameterNameValueType::TextType: param.SetValueText(StringUtils::ConvertMBSToWCS(metric.m_String), (int) metric.m_String.length()); break; case ParameterNameValueType::AsciiType: if (metric.m_String.size() > 256) { Err::errAbort("QuantMethodExprCCCHPReport: string header parameter too long, name = '" + metric.m_Name + "', value = '" + metric.m_String + "'"); } param.SetValueAscii(metric.m_String, (int) metric.m_String.length()); break; default: Err::errAbort("QuantMethodExprCCCHPReport: unknown header parameter type found in file " + filename); } updateHdr.AddNameValParam(param); } } std::ofstream os; Fs::aptOpen(os, filename, std::ios::out|std::ios::binary|std::ios::in); if (!os) { Err::errAbort("QuantMethodExprCCCHPReport: file " + filename + " could not be opened for writing"); } GenericDataHeaderUpdater updater; updater.Update(os, updateHdr, *hdr); os.close(); Verbose::progressStep(1); } } catch (...) { removeAllChps(); Err::errAbort("Error in creating final CHP output."); } Verbose::progressEnd(1, ToStr("Done.")); // Remove .tmp extension for (unsigned int i = 0; i < m_CHPFileNames.size(); i++) { std::string from = m_CHPFileNames[i] + ".tmp"; std::string to = m_CHPFileNames[i]; if (!Fs::fileRename(from.c_str(),to.c_str())) { removeAllChps(); Err::errAbort("Unable to rename '" + from + "' to '" + to + "'"); } } removeTmpChps(); return true; }
/** * Get set up for a run of reporting probesets. Often used to open file * streams and print headers to files etc. * * @param qMethod - Quantification method to be used. * @param layout - Where the probesets, probes, etc are on the chip. * * @return true if success, false otherwise. */ bool QuantMethodExprCCCHPReport::prepare(QuantMethod &qMethod, const IntensityMart &iMart) { QuantExprMethod *eMethod = dynamic_cast<QuantExprMethod *>(&qMethod); if (eMethod == NULL) { Err::errAbort("Can only use a QuantMethodExprReport with a QuantExprMethod."); } setupFileNames(iMart); int nfiles = m_CHPFileNames.size(); // Make sure our output directory exists. if (!Fs::isWriteableDir(m_Prefix.c_str()) && (Fs::mkdirPath(m_Prefix, false) != APT_OK)) { APT_ERR_ABORT("Can't make or write to directory: " + m_Prefix); } removeAllChps(); // Get CEL file GUIDs ///@todo This be computed by the engine and passed in via AnalysisInfo m_celGuids.resize(nfiles); std::string tmp_unc_name; for (int chip=0; chip<nfiles; chip++) { FusionCELData cel; try { tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]); cel.SetFileName(tmp_unc_name.c_str()); if (!cel.ReadHeader()) { Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name)); } GenericData *gdata = cel.GetGenericData(); if (gdata != NULL) { m_celGuids[chip] = gdata->Header().GetGenericDataHdr()->GetFileId(); } cel.Close(); } catch (...) { Err::errAbort("Unable to read CEL file " + tmp_unc_name); } } int maxProbeSetNameLength = 0; for (int i=0; i<m_Info.m_ProbesetNames.size(); i++) { int len = (int)strlen(m_Info.m_ProbesetNames.at(i)); if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames.at(i) != NULL) len = (int)strlen(m_Info.m_ProbesetDisplayNames.at(i)); maxProbeSetNameLength = Max(maxProbeSetNameLength, len); } // Prepare headers for all CHP files. wstring algName = StringUtils::ConvertMBSToWCS(m_Info.m_AlgName); wstring algVersion = StringUtils::ConvertMBSToWCS(m_Info.m_AlgVersion); wstring chipType = StringUtils::ConvertMBSToWCS(m_Info.m_ChipType); // For each chip, precreate all probeset signal entries (default to 0.0). Verbose::out(1,"QuantMethodExprCCCHPReport: Creating temporary files for CHP output"); for (int chip=0; chip<nfiles; chip++) { try { ParameterNameValueType param; // Create tmp chp file std::string tmp_chp_name=m_CHPFileNames[chip] + ".tmp"; CHPQuantificationData *data = new CHPQuantificationData(tmp_chp_name); m_TmpChpFiles.push_back(tmp_chp_name); // set parent header FusionCELData cel; try { tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]); cel.SetFileName(tmp_unc_name.c_str()); if (!cel.ReadHeader()) { Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name)); } GenericData *gdata = cel.GetGenericData(); if (gdata != NULL) { data->GetFileHeader()->GetGenericDataHdr()->AddParent(*gdata->Header().GetGenericDataHdr()); } cel.Close(); } catch (...) { Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name)); } data->SetEntryCount(m_Info.m_NumProbeSets, maxProbeSetNameLength); data->SetAlgName(algName); data->SetAlgVersion(algVersion); data->SetArrayType(chipType); param.SetName(L"program-name"); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramName)); data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param); param.SetName(L"program-version"); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramVersion)); data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param); param.SetName(L"program-company"); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramCompany)); data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param); // Add algorithm parameters to list. ParameterNameValueTypeList paramList; assert(m_Info.m_ParamNames.size() == m_Info.m_ParamValues.size()); for (int i=0; i<m_Info.m_ParamNames.size(); i++) { if (m_Info.m_ParamValues[i].length() > 0) { param.SetName(StringUtils::ConvertMBSToWCS(m_Info.m_ParamNames[i])); param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ParamValues[i])); paramList.push_back(param); } } // Add list of all CEL GUIDs in batch ///@todo should this be computed by the engine and passed in via AnalysisInfo? string prefix = "apt-opt-"; for (int chip=0; chip<m_CHPFileNames.size(); chip++) { if (m_celGuids[chip].empty() == false) { string paramName = prefix + "cel-guid-" + ToStr(chip+1); param.SetName(StringUtils::ConvertMBSToWCS(paramName)); param.SetValueText(StringUtils::ConvertMBSToWCS(m_celGuids[chip])); paramList.push_back(param); } } data->AddAlgParams(paramList); // Add the run report parameters to the list ParameterNameValueTypeList summaryParamList; std::string blankStr(256, ' '); for (int source=0; source<m_ChipSummaries.size(); source++) { ChipSummary::metricDefVec_t metricDefs = m_ChipSummaries[source]->getMetricDefs(); for (int i = 0; i < metricDefs.size(); i++) { param.SetName(StringUtils::ConvertMBSToWCS(metricDefs[i].m_name)); if (metricDefs[i].m_type == ChipSummary::Metric::Double) { param.SetValueFloat(-1.0); } else if (metricDefs[i].m_type == ChipSummary::Metric::Integer) { param.SetValueInt32(-1); } else if (metricDefs[i].m_type == ChipSummary::Metric::String) { param.SetValueAscii(blankStr); } else { Err::errAbort("QuantMethodExprCCCHPReport: Unable to handle unknown type: " + ToStr(metricDefs[i].m_type) ); } summaryParamList.push_back(param); } } data->AddSummaryParams(summaryParamList); ProbeSetQuantificationData entry; CHPQuantificationFileWriter writer(*data); writer.SeekToDataSet(); // seek to data table location for (int index=0; index<m_Info.m_ProbesetNames.size(); index++) { if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames[index] != NULL) entry.name = m_Info.m_ProbesetDisplayNames[index]; else entry.name = m_Info.m_ProbesetNames[index]; entry.quantification = 0.0f; writer.WriteEntry(entry); } delete data; } catch (...) { Err::errAbort("QuantMethodExprCHPReport::prepare() - Unable to write header and/or precreate signal entries to file: " + m_CHPFileNames[chip] + ".tmp"); } } // initialize expression signal buffer writer m_ExpressionQuantificationBufferWriter.Initialize(&m_TmpChpFiles); return true; }
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile2() { CHPMultiDataData data(TEST2_FILE); vector<ColumnInfo> cols; ParameterNameValueType nv; ByteColumn bcol(L"byte"); cols.push_back(bcol); UByteColumn ubcol(L"ubyte"); cols.push_back(ubcol); ShortColumn scol(L"short"); cols.push_back(scol); UShortColumn uscol(L"ushort"); cols.push_back(uscol); IntColumn icol(L"int"); cols.push_back(icol); UIntColumn uicol(L"uint"); cols.push_back(uicol); FloatColumn fcol(L"float"); cols.push_back(fcol); ASCIIColumn acol(L"ascii", 7); cols.push_back(acol); UnicodeColumn tcol(L"text", 10); cols.push_back(tcol); ProbeSetMultiDataGenotypeData e; data.SetEntryCount(GenotypeMultiDataType, 4, 10, cols); CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data); nv.SetName(L"byte"); nv.SetValueInt8(8); e.metrics.push_back(nv); nv.SetName(L"ubyte"); nv.SetValueUInt8(8); e.metrics.push_back(nv); nv.SetName(L"short"); nv.SetValueInt16(16); e.metrics.push_back(nv); nv.SetName(L"ushort"); nv.SetValueUInt16(16); e.metrics.push_back(nv); nv.SetName(L"int"); nv.SetValueInt32(32); e.metrics.push_back(nv); nv.SetName(L"uint"); nv.SetValueUInt32(32); e.metrics.push_back(nv); nv.SetName(L"float"); nv.SetValueFloat(44.0f); e.metrics.push_back(nv); nv.SetName(L"ascii"); nv.SetValueAscii("ascii"); e.metrics.push_back(nv); nv.SetName(L"text"); nv.SetValueText(L"text"); e.metrics.push_back(nv); writer->SeekToDataSet(GenotypeMultiDataType); e.name = "1"; e.call = 1; e.confidence = 10.0f; writer->WriteEntry(e); e.name = "2"; e.call = 2; e.confidence = 20.0f; writer->WriteEntry(e); e.name = "3"; e.call = 3; e.confidence = 30.0f; writer->WriteEntry(e); e.name = "4"; e.call = 4; e.confidence = 40.0f; writer->WriteEntry(e); delete writer; }
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile3() { CHPMultiDataData data(TEST3_FILE); vector<ColumnInfo> cols; ParameterNameValueType nv; ByteColumn bcol(L"byte"); cols.push_back(bcol); UByteColumn ubcol(L"ubyte"); cols.push_back(ubcol); ShortColumn scol(L"short"); cols.push_back(scol); UShortColumn uscol(L"ushort"); cols.push_back(uscol); IntColumn icol(L"int"); cols.push_back(icol); UIntColumn uicol(L"uint"); cols.push_back(uicol); FloatColumn fcol(L"float"); cols.push_back(fcol); ASCIIColumn acol(L"ascii", 7); cols.push_back(acol); UnicodeColumn tcol(L"text", 10); cols.push_back(tcol); ProbeSetMultiDataCopyNumberData e; ProbeSetMultiDataCytoRegionData c; data.SetEntryCount(CopyNumberMultiDataType, 4, 10, cols); data.SetEntryCount(CytoMultiDataType, 2, 10); CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data); nv.SetName(L"byte"); nv.SetValueInt8(8); e.metrics.push_back(nv); nv.SetName(L"ubyte"); nv.SetValueUInt8(8); e.metrics.push_back(nv); nv.SetName(L"short"); nv.SetValueInt16(16); e.metrics.push_back(nv); nv.SetName(L"ushort"); nv.SetValueUInt16(16); e.metrics.push_back(nv); nv.SetName(L"int"); nv.SetValueInt32(32); e.metrics.push_back(nv); nv.SetName(L"uint"); nv.SetValueUInt32(32); e.metrics.push_back(nv); nv.SetName(L"float"); nv.SetValueFloat(44.0f); e.metrics.push_back(nv); nv.SetName(L"ascii"); nv.SetValueAscii("ascii"); e.metrics.push_back(nv); nv.SetName(L"text"); nv.SetValueText(L"text"); e.metrics.push_back(nv); writer->SeekToDataSet(CopyNumberMultiDataType); e.name = "1"; e.chr = 1; e.position = 10; writer->WriteEntry(e); e.name = "2"; e.chr = 2; e.position = 20; writer->WriteEntry(e); e.name = "3"; e.chr = 3; e.position = 30; writer->WriteEntry(e); e.name = "4"; e.chr = 4; e.position = 40; writer->WriteEntry(e); writer->SeekToDataSet(CytoMultiDataType); c.name = "1"; c.chr= 1; c.startPosition = 1; c.stopPosition = 2; c.call = 1; c.confidenceScore = 10.0f; writer->WriteEntry(c); c.name = "2"; c.chr= 2; c.startPosition = 2; c.stopPosition = 3; c.call = 2; c.confidenceScore = 20.0f; writer->WriteEntry(c); delete writer; }
void TestFileGenerator::WriteLargeCelFile() { CelFileData data("large_cel_file"); data.SetRows(2560); data.SetCols(2560); int32_t cells = 2560*2560; data.SetIntensityCount(cells); data.SetStdDevCount(cells); data.SetPixelCount(cells); data.SetOutlierCount(2000); data.SetMaskCount(3000); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; FloatVector vStdev; Int16Vector vPixels; vInten.resize(cells); vStdev.resize(cells); vPixels.resize(cells); int32_t intenTestValues[4] = {55683.0f, 4568.0f, 2368.0f, 100.0f}; float stdevTestValues[4] = {2.345f, 56.23f, 1.53f, 3.875f}; //int32_t testIdx = 0; for (int32_t i=0, testIdx=0; i<cells; ++i, ++testIdx) { if (testIdx >= 4) testIdx = 0; vInten[i] = intenTestValues[testIdx]; vStdev[i] = stdevTestValues[testIdx]; vPixels[i] = 25; } // Do some writing writer->WriteIntensities(vInten); writer->WriteStdDevs(vStdev); writer->WritePixels(vPixels); XYCoord xy(0,0); XYCoordVector outlier; for (int32_t i=0, col=2000; i<2000; ++i, --col) { xy.xCoord = i; xy.yCoord = col; outlier.push_back(xy); } writer->WriteOutlierCoords(outlier); XYCoordVector masked; for (int32_t i=0; i<1500; ++i) { xy.xCoord = 1200; xy.yCoord = i; masked.push_back(xy); xy.xCoord = 2400; xy.yCoord = i; masked.push_back(xy); } writer->WriteMaskCoords(masked); delete writer; }
void TestFileGenerator::WriteRemaingSmallCelFileWithGridParameters(CelFileData& data) { data.SetIntensityCount(25); data.SetStdDevCount(25); data.SetPixelCount(25); data.SetOutlierCount(2); data.SetMaskCount(3); data.SetRows(5); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetLibraryPackageName(L"Hg-small-lib-package"); data.SetMasterFileName(L"Hg-small-master-file"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"CellMargin"); nvt.SetValueInt32(2); data.AddAlgorithmParameter(nvt); // Add grid wchar_t* gridParams[] = {L"GridULX", L"GridULY", L"GridURX", L"GridURY", L"GridLRX", L"GridLRY", L"GridLLX", L"GridLLY" }; for (int32_t i = 0; i < 8; ++i) { nvt.SetName(gridParams[i]); nvt.SetValueFloat(2.0f + (float)i); data.AddAlgorithmParameter(nvt); } CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; FloatVector vStdev; Int16Vector vPixels; for (int i=0; i<25; ++i) { vInten.push_back(100.0f*i); vStdev.push_back(.5*i); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WriteStdDevs(vStdev); writer->WritePixels(vPixels); // XYCoordVector XYCoordVector outlier; XYCoord xy(0,0); outlier.push_back(xy); xy.xCoord = 1; xy.yCoord = 2; outlier.push_back(xy); writer->WriteOutlierCoords(outlier); XYCoordVector masked; xy.xCoord = 1; xy.yCoord = 0; masked.push_back(xy); xy.xCoord = 2; xy.yCoord = 1; masked.push_back(xy); xy.xCoord = 3; xy.yCoord = 2; masked.push_back(xy); writer->WriteMaskCoords(masked); delete writer; }
void TestFileGenerator::WriteOutGenericDATDataFileWithGrid() { GenericDataHeader gdh; AddStandardGenericDataHeader(gdh); // Fill the DataGroupHeader DataGroupHeader dch; dch.SetName(L""); // unnamed DataGroup // Fill the pixel intensity DataSetHeader DataSetHeader dphPixel; dphPixel.SetName(L"acquired data"); ParameterNameValueType nvt; nvt.SetName(L"Scanner"); nvt.SetValueText(L"M10"); dphPixel.AddNameValParam(nvt); nvt.SetName(L"Pixel Size"); nvt.SetValueFloat(0.051f); dphPixel.AddNameValParam(nvt); dphPixel.AddColumn(UShortColumn(L"Pixel")); int32_t rows = 1000; dphPixel.SetRowCnt(rows); dch.AddDataSetHdr(dphPixel); // Fill the grid DataSetHeader DataSetHeader dphGrid; dphGrid.SetName(L"grid position"); nvt.SetName(L"GhostGrids"); nvt.SetValueText(L"True"); dphGrid.AddNameValParam(nvt); nvt.SetName(L"Pixel Size"); nvt.SetValueFloat(0.051f); dphGrid.AddNameValParam(nvt); dphGrid.AddColumn(FloatColumn(L"Upper left x")); dphGrid.AddColumn(FloatColumn(L"Upper left y")); dphGrid.AddColumn(FloatColumn(L"Upper right x")); dphGrid.AddColumn(FloatColumn(L"Upper right y")); dphGrid.AddColumn(FloatColumn(L"Lower right x")); dphGrid.AddColumn(FloatColumn(L"Lower right y")); dphGrid.AddColumn(FloatColumn(L"Lower left x")); dphGrid.AddColumn(FloatColumn(L"Lower left y")); int32_t grids = 5; // first is the global grid with 4 subgrids dphGrid.SetRowCnt(grids); dch.AddDataSetHdr(dphGrid); // Set the FileHeader FileHeader fh; fh.SetFilename("test.file.data_dat_with_grid"); fh.SetGenericDataHdr(gdh); fh.AddDataGroupHdr(dch); // Create the generic file writer GenericFileWriter gfWriter(&fh); gfWriter.WriteHeader(); DataGroupWriterIt dcwBegin, dcwEnd; gfWriter.GetDataGroupWriters(dcwBegin, dcwEnd); DataGroupWriter d = *dcwBegin; dcwBegin->WriteHeader(); DataSetWriterIt dpwBegin, dpwEnd; dcwBegin->GetDataSetWriters(dpwBegin, dpwEnd); // Write out the pixel DataSet dpwBegin->WriteHeader(); for( int32_t i=0; i < rows; ++i ) { u_int16_t value = (u_int16_t)(i*10+i); dpwBegin->Write(value); } dpwBegin->UpdateNextDataSetOffset(); ++dpwBegin; // Write out the grid DataSet dpwBegin->WriteHeader(); for( int32_t i=0; i < grids; ++i ) { for (int32_t corner = 0; corner < 4; ++corner) { float value = (float)(i*100 + corner); dpwBegin->Write(value); dpwBegin->Write(value); } } dpwBegin->UpdateNextDataSetOffset(); dcwBegin->Close(); }
// Uses a mix of the GenericFileWriter and raw commands void TestFileGenerator::WriteOutGenericDATDataFile1UsingGenericWriter() { GenericDataHeader gdh; AddStandardGenericDataHeader(gdh); // Fill the DataSetHeader DataSetHeader dph; dph.SetName(L"acquired data"); ParameterNameValueType nvt; nvt.SetName(L"Scanner"); nvt.SetValueText(L"M10"); dph.AddNameValParam(nvt); nvt.SetName(L"Pixel Size"); nvt.SetValueFloat(0.051f); dph.AddNameValParam(nvt); dph.AddColumn(UShortColumn(L"Pixel")); int32_t rows = 100; dph.SetRowCnt(rows); // Open the file. ofstream fileStream; fileStream.open( "test.file.data_dat", ios_base::out | ios_base::binary | ios_base::trunc); // Write the file header using raw methods until the writer is available. // magic number FileOutput::WriteUInt8(fileStream, 59); // version FileOutput::WriteInt8(fileStream, 1); // Number of data cubes - confirm this FileOutput::WriteUInt32(fileStream, 1); // offset to the data cube byte offset array int offsetLocation = fileStream.tellp(); FileOutput::WriteUInt32(fileStream, 1); //???? // Write the GenericDataHeader to the file GenericDataHeaderWriter gdhWriter; gdhWriter.Write(fileStream, gdh); // // Data Cube // int offset = fileStream.tellp(); // Write the DataSetHeader DataSetWriter dphWriter(&fileStream, &dph); dphWriter.WriteHeader(); // Write out the data for( int32_t i=0; i < rows; ++i ) { u_int16_t value = (u_int16_t)(i*10+i); FileOutput::WriteUInt16(fileStream, value); } // write the offset fileStream.seekp(offsetLocation); FileOutput::WriteUInt32(fileStream, offset); fileStream.close(); }